Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536810027984/tk2689sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536810027984/tk2689Isup2.hkl |
CCDC reference: 788259
Key indicators
- Single-crystal X-ray study
- T = 173 K
- Mean (C-C) = 0.006 Å
- R factor = 0.044
- wR factor = 0.118
- Data-to-parameter ratio = 15.6
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang .. 6 PLAT910_ALERT_3_C Missing # of FCF Reflections Below Th(Min) ..... 3 PLAT042_ALERT_1_C Calc. and Reported MoietyFormula Strings Differ ? PLAT912_ALERT_4_C Missing # of FCF Reflections Above STh/L= 0.600 2
Alert level G REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF. From the CIF: _diffrn_reflns_theta_max 27.47 From the CIF: _reflns_number_total 2138 Count of symmetry unique reflns 1303 Completeness (_total/calc) 164.08% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 835 Fraction of Friedel pairs measured 0.641 Are heavy atom types Z>Si present yes PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 9 N1 -C4 -C5 -K1 52.00 2.00 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 10 C6 -C4 -C5 -K1 -67.50 1.90 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 81 C5 -O2 -K1 -O4 -45.10 1.70 1.555 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 82 K1 -O2 -K1 -O4 72.80 1.60 1.655 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 83 K1 -O2 -K1 -O4 18.00 0.00 3.567 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 102 C4 -C5 -K1 -O2 -16.80 1.80 1.555 1.555 1.555 1.455 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 105 C4 -C5 -K1 -O3 -87.60 1.80 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 109 C4 -C5 -K1 -O2 62.80 1.80 1.555 1.555 1.555 3.467 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 113 C4 -C5 -K1 -O4 166.50 1.80 1.555 1.555 1.555 3.467 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 116 C4 -C5 -K1 -O2 103.30 1.90 1.555 1.555 1.555 1.555 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 120 C4 -C5 -K1 -O4 -82.00 1.90 1.555 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 124 C4 -C5 -K1 -C7 123.70 1.80 1.555 1.555 1.555 3.467 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 126 O2 -C5 -K1 -C8 154.00 2.00 1.555 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 127 O3 -C5 -K1 -C8 -15.00 2.00 1.555 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 128 C4 -C5 -K1 -C8 -103.00 3.00 1.555 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 129 K1 -C5 -K1 -C8 110.00 2.00 1.655 1.555 1.555 3.367 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 132 C4 -C5 -K1 -C5 -33.00 1.90 1.555 1.555 1.555 1.455 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 136 C4 -C5 -K1 -C8 149.40 1.80 1.555 1.555 1.555 3.467 PLAT710_ALERT_4_G Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # 140 C4 -C5 -K1 -K1 73.40 1.80 1.555 1.555 1.555 3.567 PLAT764_ALERT_4_G Overcomplete CIF Bond List Detected (Rep/Expd) . 1.24 Ratio PLAT779_ALERT_4_G Suspect or Irrelevant (Bond) Angle in CIF ...... 44.80 Deg. O2 -C5 -K1 1.555 1.555 1.655 PLAT791_ALERT_4_G Note: The Model has Chirality at C3 (Verify) R PLAT791_ALERT_4_G Note: The Model has Chirality at C4 (Verify) R PLAT804_ALERT_5_G ARU-Pack Problem in PLATON Analysis ............ 14 Times
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 4 ALERT level C = Check and explain 25 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 0 ALERT type 2 Indicator that the structure model may be wrong or deficient 2 ALERT type 3 Indicator that the structure quality may be low 25 ALERT type 4 Improvement, methodology, query or suggestion 1 ALERT type 5 Informative message, check
checkCIF publication errors
Alert level A PUBL024_ALERT_1_A The number of authors is greater than 5. Please specify the role of each of the co-authors for your paper.
Author Response: As a result of crystallographic and pharmaceutical study of two international group, the number of authors became eight. The list of author's contribution is following. |
Dr. Kotaro Fujii discussed on the structure. Mr. Kazuyuki Toyota analyzed the crystal structure. Dr. Akiko Sekinse is responsible for the low temperature crystallization. Dr. Hidehiro Uekusa is responsible of this international corroboration work. Dr. Ilma Nugrahani is responsible for the Indonesian group and also is studying on the hydrolysis of this compound with Dr. Sukmadjaja. Dr. N. Sundani Soewandhi and Slamet Ilbrahim are responsible for the pharmaceutical activity study of this compound.
1 ALERT level A = Data missing that is essential or data in wrong format 0 ALERT level G = General alerts. Data that may be required is missing
The single crystals of potassium clavulanate were grown at a low temperature in order to prevent decomposition. After the compound was dissolved into an 8:2 mixture of methanol/water, a few drops of 1-propanol were added to the solution and the solution was kept at 235 K for a few days. The crystal used in the analysis was immediately covered with inert oil in order to prevent the decomposition through contact with atmospheric water vapor.
The O- and C-bound H atoms were geometrically placed (O–H = 0.84 Å and C–H = 0.95–1.00 Å,) and refined as riding with Uiso(H) = 1.2Ueq(carrier atom). The absolute structure was assigned according to the known configuration of the acid, an assignment confirmed by the refinement of the Flack parameter (Flack, 1983).
Many pathogenic bacteria secrete β-lactamases as a defense mechanism against β-lactam antibiotics. Because such β-lactamases have the potential to inactivate β-lactam antibiotics, inhibitors for these β-lactamases are clinically very important. Clavulanic acid (CA) is a powerful naturally obtained inhibitor for bacterial β-lactamases produced by the organism Streptomyces clavuligerus. Although CA itself can act as an β-lactam antibiotic and is active against a wide spectrum of Gram-positive and Gram-negative bacteria (Mayer & Deckwer, 1996), it is much more effective as a drug in combination with β-lactamase-sensitive penicillins, such as amoxicillin. In that situation, CA protects the β-lactam ring of the amoxicillin from hydrolysis and can maintain its activity against β-lactamase producing bacteria (Bird et al., 1982). The CA potassium salt is widely used as a drug in injectable and solid form, especially combined with amoxicillin sodium and amoxicillin trihydrate (Navarro, 2005).
In this context, an understanding of the structure of CA is important in order to establish its ability to form molecular interactions. Unfortunately, CA is chemically unstable as are the other β-lactam antibiotics, being very sensitive to pH, temperature, and humidity via the hydrolysis degradation mechanism; (Bersanetti et al., 2005; Hickey et al., 2007; Saudagar et al., 2008). The decomposition is also self-catalyzed (Brethauer et al. 2008; Haginaka et al. 1985) and there have been some difficulties in obtaining a single crystals of CA. Therefore, until now there has been no report of a crystal structure of CA. In this study, single crystals of potassium clavulanate were successfully obtained by a low-temperature crystallization process and the crystal structure was determined.
In the molecular structure of potassium clavulanate, Fig. 1, the C5–O2 and C5–O3 distances of 1.262 (5)Å and 1.256 (5) Å, respectively, indicate that the negative charge of the carboxylate group is delocalised. The potassium cation is surrounded by six oxygen atoms, three O2, one O3 and two O4, deriv ed from four different clavulanate anions. The selected bond lengths around the potassium cation are listed in Table 1. These interactions are infinitely linked along the a axis and lead to an ionic (hydrophilic) column structure. These columns are connected by intermolecular O–H···O hydrogen bonds formed between O4-hydroxyl groups and carboxylate-O2 atoms, and form a hydrophobic layer in the ab plane; Fig. 2. By contrast, the remaining hydrophobic groups (i.e. bicyclo groups) form a hydrophobic layer so that the crystal structure comprises alternating hydrophilic and hydrophilic regions.
For the pharmacological activity of clavulanic acid and potassium clavulanate, see: Bird et al. (1982); Mayer & Deckwer (1996); Navarro (2005). For the hydrolysis properties of clavulanic acid and potassium clavulanate, see: Bersanetti et al. (2005); Brethauer et al. (2008); Haginaka et al. (1985); Hickey et al. (2007); Saudagar et al. (2008).
Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: PROCESS-AUTO (Rigaku, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).
K+·C8H8NO5− | F(000) = 488 |
Mr = 237.25 | Dx = 1.687 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71075 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 9047 reflections |
a = 4.3453 (6) Å | θ = 3.0–27.5° |
b = 7.8191 (11) Å | µ = 0.57 mm−1 |
c = 27.491 (3) Å | T = 173 K |
V = 934.1 (2) Å3 | Platet, colorless |
Z = 4 | 0.24 × 0.04 × 0.01 mm |
Rigaku R-AXIS RAPID IP area-detector diffractometer | 2138 independent reflections |
Radiation source: rotating anode, Rigaku UltraX18 | 1433 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.088 |
ω scan | θmax = 27.5°, θmin = 3.0° |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | h = −5→5 |
Tmin = 0.876, Tmax = 0.994 | k = −10→10 |
9047 measured reflections | l = −35→35 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.044 | H-atom parameters constrained |
wR(F2) = 0.118 | w = 1/[σ2(Fo2) + (0.0305P)2 + 0.8726P] where P = (Fo2 + 2Fc2)/3 |
S = 1.12 | (Δ/σ)max = 0.001 |
2138 reflections | Δρmax = 0.52 e Å−3 |
137 parameters | Δρmin = −0.56 e Å−3 |
0 restraints | Absolute structure: Flack (1983), 839 Friedel pairs |
Primary atom site location: structure-invariant direct methods | Absolute structure parameter: −0.05 (9) |
K+·C8H8NO5− | V = 934.1 (2) Å3 |
Mr = 237.25 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 4.3453 (6) Å | µ = 0.57 mm−1 |
b = 7.8191 (11) Å | T = 173 K |
c = 27.491 (3) Å | 0.24 × 0.04 × 0.01 mm |
Rigaku R-AXIS RAPID IP area-detector diffractometer | 2138 independent reflections |
Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | 1433 reflections with I > 2σ(I) |
Tmin = 0.876, Tmax = 0.994 | Rint = 0.088 |
9047 measured reflections |
R[F2 > 2σ(F2)] = 0.044 | H-atom parameters constrained |
wR(F2) = 0.118 | Δρmax = 0.52 e Å−3 |
S = 1.12 | Δρmin = −0.56 e Å−3 |
2138 reflections | Absolute structure: Flack (1983), 839 Friedel pairs |
137 parameters | Absolute structure parameter: −0.05 (9) |
0 restraints |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
C1 | 1.2101 (11) | 0.3967 (6) | 1.20066 (15) | 0.0297 (11) | |
C2 | 1.1168 (11) | 0.5309 (6) | 1.23813 (13) | 0.0276 (9) | |
H2A | 1.2901 | 0.5798 | 1.2569 | 0.033* | |
H2B | 0.9447 | 0.4964 | 1.2596 | 0.033* | |
C3 | 1.0199 (11) | 0.6369 (6) | 1.19340 (14) | 0.0250 (10) | |
H3 | 0.8027 | 0.6790 | 1.1942 | 0.030* | |
C4 | 1.2417 (9) | 0.5363 (6) | 1.11851 (13) | 0.0192 (8) | |
H4 | 1.4273 | 0.4611 | 1.1163 | 0.023* | |
C5 | 1.0676 (9) | 0.5213 (6) | 1.06982 (13) | 0.0201 (8) | |
C6 | 1.3526 (11) | 0.7148 (5) | 1.13197 (12) | 0.0218 (9) | |
C7 | 1.5398 (10) | 0.8175 (6) | 1.10754 (14) | 0.0245 (10) | |
H7 | 1.6169 | 0.7752 | 1.0775 | 0.029* | |
C8 | 1.6419 (11) | 0.9914 (5) | 1.12198 (13) | 0.0269 (9) | |
H8A | 1.5056 | 1.0382 | 1.1476 | 0.032* | |
H8B | 1.8551 | 0.9881 | 1.1346 | 0.032* | |
O1 | 1.3545 (10) | 0.2661 (4) | 1.20053 (11) | 0.0458 (9) | |
O2 | 1.1415 (8) | 0.6217 (4) | 1.03630 (9) | 0.0258 (7) | |
O3 | 0.8682 (9) | 0.4058 (4) | 1.06647 (10) | 0.0318 (7) | |
O4 | 1.6262 (9) | 1.0947 (4) | 1.07905 (10) | 0.0321 (8) | |
H4A | 1.6958 | 1.1926 | 1.0851 | 0.038* | |
O5 | 1.2401 (7) | 0.7604 (4) | 1.17783 (9) | 0.0266 (7) | |
N1 | 1.0715 (8) | 0.4860 (5) | 1.16197 (10) | 0.0242 (8) | |
K1 | 0.6334 (2) | 0.52404 (13) | 0.97836 (3) | 0.0284 (2) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.036 (3) | 0.027 (2) | 0.026 (2) | −0.001 (2) | 0.001 (2) | 0.0026 (19) |
C2 | 0.029 (2) | 0.035 (2) | 0.0185 (16) | −0.001 (3) | −0.0026 (18) | 0.0049 (18) |
C3 | 0.026 (2) | 0.025 (2) | 0.024 (2) | 0.0001 (19) | 0.0021 (19) | 0.0033 (18) |
C4 | 0.0183 (18) | 0.018 (2) | 0.0211 (17) | −0.0025 (18) | −0.0009 (15) | 0.0023 (17) |
C5 | 0.017 (2) | 0.022 (2) | 0.0214 (17) | −0.0007 (18) | 0.0031 (15) | −0.0040 (17) |
C6 | 0.020 (2) | 0.028 (2) | 0.0174 (17) | 0.001 (2) | −0.0018 (18) | −0.0019 (16) |
C7 | 0.027 (2) | 0.026 (2) | 0.0204 (18) | −0.0043 (19) | 0.0037 (18) | 0.0005 (17) |
C8 | 0.030 (2) | 0.025 (2) | 0.0255 (18) | −0.003 (2) | −0.002 (2) | 0.0008 (18) |
O1 | 0.070 (3) | 0.033 (2) | 0.0340 (16) | 0.020 (2) | 0.006 (2) | 0.0063 (15) |
O2 | 0.0265 (16) | 0.0296 (17) | 0.0213 (12) | −0.0041 (16) | −0.0002 (13) | 0.0045 (12) |
O3 | 0.0366 (19) | 0.0304 (17) | 0.0285 (14) | −0.0127 (16) | −0.0071 (15) | 0.0038 (13) |
O4 | 0.046 (2) | 0.0201 (15) | 0.0304 (15) | −0.0063 (17) | −0.0020 (17) | 0.0034 (12) |
O5 | 0.0328 (18) | 0.0248 (17) | 0.0221 (13) | −0.0045 (13) | 0.0064 (13) | −0.0013 (13) |
N1 | 0.032 (2) | 0.0236 (19) | 0.0174 (14) | 0.0030 (17) | 0.0036 (14) | 0.0043 (14) |
K1 | 0.0242 (4) | 0.0362 (5) | 0.0248 (4) | 0.0008 (5) | −0.0007 (4) | 0.0031 (4) |
C1—O1 | 1.199 (6) | C7—H7 | 0.9500 |
C1—N1 | 1.408 (5) | C8—O4 | 1.432 (5) |
C1—C2 | 1.525 (6) | C8—H8A | 0.9900 |
C2—C3 | 1.542 (5) | C8—H8B | 0.9900 |
C2—H2A | 0.9900 | O4—H4A | 0.8400 |
C2—H2B | 0.9900 | O2—K1i | 2.773 (3) |
C3—O5 | 1.425 (5) | O2—K1ii | 2.799 (3) |
C3—N1 | 1.480 (5) | O2—K1 | 2.827 (3) |
C3—H3 | 1.0000 | O3—K1 | 2.786 (3) |
C4—N1 | 1.459 (5) | O4—K1ii | 2.818 (4) |
C4—C6 | 1.522 (6) | O4—K1iii | 2.865 (4) |
C4—C5 | 1.542 (5) | O4—H4A | 0.8400 |
C4—H4 | 1.0000 | K1—O2iv | 2.773 (3) |
C5—O2 | 1.252 (5) | K1—O2v | 2.799 (3) |
C5—O3 | 1.256 (5) | K1—O4v | 2.818 (4) |
C6—C7 | 1.325 (6) | K1—O4vi | 2.865 (4) |
C6—O5 | 1.398 (4) | K1—C7v | 3.198 (4) |
C7—C8 | 1.485 (6) | ||
O1—C1—N1 | 130.1 (4) | C1—N1—C4 | 122.4 (4) |
O1—C1—C2 | 136.7 (4) | C1—N1—C3 | 91.1 (3) |
N1—C1—C2 | 93.2 (3) | C4—N1—C3 | 109.9 (3) |
C1—C2—C3 | 84.5 (3) | O2iv—K1—O3 | 82.78 (10) |
C1—C2—H2A | 114.6 | O2iv—K1—O2v | 79.62 (9) |
C3—C2—H2A | 114.6 | O3—K1—O2v | 116.68 (9) |
C1—C2—H2B | 114.6 | O2iv—K1—O4v | 176.73 (10) |
C3—C2—H2B | 114.6 | O3—K1—O4v | 95.70 (10) |
H2A—C2—H2B | 111.7 | O2v—K1—O4v | 103.64 (9) |
O5—C3—N1 | 105.3 (3) | O2iv—K1—O2 | 101.77 (9) |
O5—C3—C2 | 114.9 (4) | O3—K1—O2 | 46.69 (9) |
N1—C3—C2 | 89.7 (3) | O2v—K1—O2 | 78.70 (9) |
O5—C3—H3 | 114.7 | O4v—K1—O2 | 79.11 (9) |
N1—C3—H3 | 114.7 | O2iv—K1—O4vi | 79.21 (9) |
C2—C3—H3 | 114.7 | O3—K1—O4vi | 130.76 (10) |
N1—C4—C6 | 102.0 (3) | O2v—K1—O4vi | 104.54 (9) |
N1—C4—C5 | 116.2 (3) | O4v—K1—O4vi | 99.74 (9) |
C6—C4—C5 | 115.9 (3) | O2—K1—O4vi | 176.76 (10) |
N1—C4—H4 | 107.4 | O2iv—K1—C5 | 90.29 (9) |
C6—C4—H4 | 107.4 | O3—K1—C5 | 23.47 (10) |
C5—C4—H4 | 107.4 | O2v—K1—C5 | 96.56 (11) |
O2—C5—O3 | 125.0 (3) | O4v—K1—C5 | 89.41 (10) |
O2—C5—C4 | 117.7 (4) | O2—K1—C5 | 23.45 (9) |
O3—C5—C4 | 117.2 (3) | O4vi—K1—C5 | 154.16 (10) |
O2—C5—K1 | 64.0 (2) | O2iv—K1—C7v | 137.98 (11) |
O3—C5—K1 | 62.1 (2) | O3—K1—C7v | 124.63 (12) |
C4—C5—K1 | 171.2 (3) | O2v—K1—C7v | 60.23 (10) |
O2—C5—K1i | 44.8 (2) | O4v—K1—C7v | 45.13 (10) |
O3—C5—K1i | 115.7 (3) | O2—K1—C7v | 83.12 (10) |
C4—C5—K1i | 106.1 (2) | O4vi—K1—C7v | 98.25 (10) |
K1—C5—K1i | 81.24 (8) | C5—K1—C7v | 105.17 (11) |
C7—C6—O5 | 121.1 (4) | O2iv—K1—C8vi | 89.53 (10) |
C7—C6—C4 | 128.8 (4) | O3—K1—C8vi | 154.09 (11) |
O5—C6—C4 | 110.0 (3) | O2v—K1—C8vi | 85.89 (9) |
C6—C7—C8 | 127.1 (4) | O4v—K1—C8vi | 90.62 (10) |
C6—C7—K1ii | 105.7 (3) | O2—K1—C8vi | 158.79 (11) |
C8—C7—K1ii | 90.4 (2) | O4vi—K1—C8vi | 23.49 (9) |
C6—C7—H7 | 116.5 | C5—K1—C8vi | 177.48 (12) |
C8—C7—H7 | 116.5 | C7v—K1—C8vi | 76.57 (11) |
K1ii—C7—H7 | 71.9 | O2iv—K1—C5iv | 18.57 (9) |
O4—C8—C7 | 106.4 (3) | O3—K1—C5iv | 68.43 (10) |
O4—C8—K1iii | 52.9 (2) | O2v—K1—C5iv | 96.76 (10) |
C7—C8—K1iii | 86.5 (2) | O4v—K1—C5iv | 158.42 (10) |
O4—C8—K1ii | 49.2 (2) | O2—K1—C5iv | 98.32 (9) |
C7—C8—K1ii | 64.7 (2) | O4vi—K1—C5iv | 81.62 (9) |
K1iii—C8—K1ii | 76.39 (8) | C5—K1—C5iv | 81.24 (8) |
O4—C8—H8A | 110.5 | C7v—K1—C5iv | 156.37 (11) |
C7—C8—H8A | 110.5 | C8vi—K1—C5iv | 97.88 (10) |
K1iii—C8—H8A | 160.2 | O2iv—K1—C8v | 159.90 (10) |
K1ii—C8—H8A | 101.1 | O3—K1—C8v | 115.98 (12) |
O4—C8—H8B | 110.5 | O2v—K1—C8v | 85.05 (9) |
C7—C8—H8B | 110.5 | O4v—K1—C8v | 22.62 (9) |
K1iii—C8—H8B | 72.8 | O2—K1—C8v | 87.75 (10) |
K1ii—C8—H8B | 149.1 | O4vi—K1—C8v | 92.28 (10) |
H8A—C8—H8B | 108.6 | C5—K1—C8v | 104.40 (10) |
C5—O2—K1i | 116.6 (3) | C7v—K1—C8v | 24.83 (10) |
C5—O2—K1ii | 136.3 (3) | C8vi—K1—C8v | 76.39 (8) |
K1i—O2—K1ii | 101.51 (10) | C5iv—K1—C8v | 173.89 (10) |
C5—O2—K1 | 92.6 (2) | O2iv—K1—K1ii | 90.24 (7) |
K1i—O2—K1 | 101.77 (9) | O3—K1—K1ii | 81.25 (7) |
K1ii—O2—K1 | 100.16 (10) | O2v—K1—K1ii | 39.02 (7) |
C5—O3—K1 | 94.5 (2) | O4v—K1—K1ii | 92.38 (7) |
C8—O4—K1ii | 108.2 (2) | O2—K1—K1ii | 39.68 (6) |
C8—O4—K1iii | 103.6 (3) | O4vi—K1—K1ii | 143.56 (7) |
K1ii—O4—K1iii | 99.74 (9) | C5—K1—K1ii | 58.85 (8) |
C8—O4—H4A | 109.5 | C7v—K1—K1ii | 66.94 (8) |
K1ii—O4—H4A | 133.2 | C8vi—K1—K1ii | 123.66 (8) |
K1iii—O4—H4A | 97.3 | C5iv—K1—K1ii | 99.19 (7) |
C6—O5—C3 | 109.4 (3) | C8v—K1—K1ii | 85.90 (8) |
O1—C1—C2—C3 | 168.2 (6) | C5—O2—K1—O3 | −6.0 (2) |
N1—C1—C2—C3 | −9.2 (3) | K1i—O2—K1—O3 | 111.90 (16) |
C1—C2—C3—O5 | −98.0 (4) | K1ii—O2—K1—O3 | −143.96 (16) |
C1—C2—C3—N1 | 8.8 (3) | C5—O2—K1—O2v | 138.9 (2) |
N1—C4—C5—O2 | 151.2 (4) | K1i—O2—K1—O2v | −103.25 (11) |
C6—C4—C5—O2 | 31.4 (5) | K1ii—O2—K1—O2v | 0.89 (9) |
N1—C4—C5—O3 | −30.8 (6) | C5—O2—K1—O4v | −114.7 (3) |
C6—C4—C5—O3 | −150.6 (4) | K1i—O2—K1—O4v | 3.21 (10) |
N1—C4—C5—K1 | 52 (2) | K1ii—O2—K1—O4v | 107.35 (10) |
C6—C4—C5—K1 | −67.5 (19) | C5—O2—K1—O4vi | −45.1 (17) |
N1—C4—C5—K1i | −161.8 (3) | K1i—O2—K1—O4vi | 72.8 (16) |
C6—C4—C5—K1i | 78.4 (4) | K1ii—O2—K1—O4vi | 177 (45) |
N1—C4—C6—C7 | 174.2 (4) | K1i—O2—K1—C5 | 117.9 (3) |
C5—C4—C6—C7 | −58.6 (6) | K1ii—O2—K1—C5 | −138.0 (3) |
N1—C4—C6—O5 | −2.6 (4) | C5—O2—K1—C7v | −160.2 (3) |
C5—C4—C6—O5 | 124.7 (4) | K1i—O2—K1—C7v | −42.33 (11) |
O5—C6—C7—C8 | −3.7 (7) | K1ii—O2—K1—C7v | 61.82 (11) |
C4—C6—C7—C8 | 179.9 (4) | C5—O2—K1—C8vi | −176.9 (3) |
O5—C6—C7—K1ii | −106.5 (4) | K1i—O2—K1—C8vi | −59.1 (3) |
C4—C6—C7—K1ii | 77.1 (5) | K1ii—O2—K1—C8vi | 45.1 (3) |
C6—C7—C8—O4 | −137.0 (5) | C5—O2—K1—C5iv | 43.6 (2) |
K1ii—C7—C8—O4 | −26.9 (3) | K1i—O2—K1—C5iv | 161.47 (10) |
C6—C7—C8—K1iii | 173.3 (5) | K1ii—O2—K1—C5iv | −94.39 (11) |
K1ii—C7—C8—K1iii | −76.57 (10) | C5—O2—K1—C8v | −135.7 (3) |
C6—C7—C8—K1ii | −110.1 (5) | K1i—O2—K1—C8v | −17.85 (11) |
O3—C5—O2—K1i | −92.7 (4) | K1ii—O2—K1—C8v | 86.29 (10) |
C4—C5—O2—K1i | 85.1 (4) | C5—O2—K1—K1ii | 138.0 (3) |
K1—C5—O2—K1i | −104.54 (19) | K1i—O2—K1—K1ii | −104.15 (11) |
O3—C5—O2—K1ii | 119.4 (4) | O2—C5—K1—O2iv | −120.1 (3) |
C4—C5—O2—K1ii | −62.7 (5) | O3—C5—K1—O2iv | 70.9 (3) |
K1—C5—O2—K1ii | 107.6 (3) | C4—C5—K1—O2iv | −16.8 (18) |
K1i—C5—O2—K1ii | −147.8 (5) | K1i—C5—K1—O2iv | −163.73 (9) |
O3—C5—O2—K1 | 11.8 (5) | O2—C5—K1—O3 | 169.1 (4) |
C4—C5—O2—K1 | −170.3 (3) | C4—C5—K1—O3 | −87.6 (18) |
K1i—C5—O2—K1 | 104.54 (19) | K1i—C5—K1—O3 | 125.4 (3) |
O2—C5—O3—K1 | −12.0 (5) | O2—C5—K1—O2v | −40.5 (2) |
C4—C5—O3—K1 | 170.1 (3) | O3—C5—K1—O2v | 150.5 (3) |
K1i—C5—O3—K1 | −63.5 (2) | C4—C5—K1—O2v | 62.8 (18) |
C7—C8—O4—K1ii | 32.7 (4) | K1i—C5—K1—O2v | −84.14 (9) |
K1iii—C8—O4—K1ii | 105.23 (18) | O2—C5—K1—O4v | 63.2 (2) |
C7—C8—O4—K1iii | −72.5 (3) | O3—C5—K1—O4v | −105.9 (3) |
K1ii—C8—O4—K1iii | −105.23 (18) | C4—C5—K1—O4v | 166.5 (18) |
C7—C6—O5—C3 | 173.7 (4) | K1i—C5—K1—O4v | 19.52 (9) |
C4—C6—O5—C3 | −9.2 (4) | O3—C5—K1—O2 | −169.1 (4) |
N1—C3—O5—C6 | 16.9 (4) | C4—C5—K1—O2 | 103.3 (19) |
C2—C3—O5—C6 | 113.9 (4) | K1i—C5—K1—O2 | −43.7 (2) |
O1—C1—N1—C4 | −53.6 (7) | O2—C5—K1—O4vi | 174.7 (2) |
C2—C1—N1—C4 | 124.1 (4) | O3—C5—K1—O4vi | 5.7 (4) |
O1—C1—N1—C3 | −168.1 (6) | C4—C5—K1—O4vi | −82.0 (19) |
C2—C1—N1—C3 | 9.6 (3) | K1i—C5—K1—O4vi | 131.1 (2) |
C6—C4—N1—C1 | −91.7 (5) | O2—C5—K1—C7v | 20.4 (3) |
C5—C4—N1—C1 | 141.3 (4) | O3—C5—K1—C7v | −148.7 (3) |
C6—C4—N1—C3 | 13.0 (4) | C4—C5—K1—C7v | 123.7 (18) |
C5—C4—N1—C3 | −114.0 (4) | K1i—C5—K1—C7v | −23.27 (12) |
O5—C3—N1—C1 | 106.3 (3) | O2—C5—K1—C8vi | 154 (2) |
C2—C3—N1—C1 | −9.5 (3) | O3—C5—K1—C8vi | −15 (2) |
O5—C3—N1—C4 | −18.9 (4) | C4—C5—K1—C8vi | −103 (3) |
C2—C3—N1—C4 | −134.7 (3) | K1i—C5—K1—C8vi | 110 (2) |
C5—O3—K1—O2iv | −107.7 (3) | O2—C5—K1—C5iv | −136.3 (2) |
C5—O3—K1—O2v | −33.2 (3) | O3—C5—K1—C5iv | 54.6 (3) |
C5—O3—K1—O4v | 75.2 (3) | C4—C5—K1—C5iv | −33.0 (19) |
C5—O3—K1—O2 | 6.0 (2) | K1i—C5—K1—C5iv | 180.0 |
C5—O3—K1—O4vi | −176.7 (2) | O2—C5—K1—C8v | 46.1 (3) |
C5—O3—K1—C7v | 37.6 (3) | O3—C5—K1—C8v | −123.0 (3) |
C5—O3—K1—C8vi | 178.5 (2) | C4—C5—K1—C8v | 149.4 (18) |
C5—O3—K1—C5iv | −120.0 (3) | K1i—C5—K1—C8v | 2.41 (12) |
C5—O3—K1—C8v | 64.7 (3) | O2—C5—K1—K1ii | −30.0 (2) |
C5—O3—K1—K1ii | −16.4 (2) | O3—C5—K1—K1ii | 161.0 (3) |
C5—O2—K1—O2iv | 62.1 (3) | C4—C5—K1—K1ii | 73.4 (18) |
K1i—O2—K1—O2iv | 180.0 | K1i—C5—K1—K1ii | −73.62 (7) |
K1ii—O2—K1—O2iv | −75.85 (11) |
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, −y+3/2, −z+2; (iii) x+3/2, −y+3/2, −z+2; (iv) x−1, y, z; (v) x−1/2, −y+3/2, −z+2; (vi) x−3/2, −y+3/2, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H4A···O3vii | 0.84 | 1.90 | 2.673 (5) | 153 |
Symmetry code: (vii) x+1, y+1, z. |
Experimental details
Crystal data | |
Chemical formula | K+·C8H8NO5− |
Mr | 237.25 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 173 |
a, b, c (Å) | 4.3453 (6), 7.8191 (11), 27.491 (3) |
V (Å3) | 934.1 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.57 |
Crystal size (mm) | 0.24 × 0.04 × 0.01 |
Data collection | |
Diffractometer | Rigaku R-AXIS RAPID IP area-detector |
Absorption correction | Multi-scan (ABSCOR; Higashi, 1995) |
Tmin, Tmax | 0.876, 0.994 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9047, 2138, 1433 |
Rint | 0.088 |
(sin θ/λ)max (Å−1) | 0.649 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.118, 1.12 |
No. of reflections | 2138 |
No. of parameters | 137 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.52, −0.56 |
Absolute structure | Flack (1983), 839 Friedel pairs |
Absolute structure parameter | −0.05 (9) |
Computer programs: PROCESS-AUTO (Rigaku, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997).
O2—K1i | 2.773 (3) | O3—K1 | 2.786 (3) |
O2—K1ii | 2.799 (3) | O4—K1ii | 2.818 (4) |
O2—K1 | 2.827 (3) | O4—K1iii | 2.865 (4) |
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, −y+3/2, −z+2; (iii) x+3/2, −y+3/2, −z+2. |
D—H···A | D—H | H···A | D···A | D—H···A |
O4—H4A···O3iv | 0.840 | 1.898 | 2.673 (5) | 152.75 |
Symmetry code: (iv) x+1, y+1, z. |
Many pathogenic bacteria secrete β-lactamases as a defense mechanism against β-lactam antibiotics. Because such β-lactamases have the potential to inactivate β-lactam antibiotics, inhibitors for these β-lactamases are clinically very important. Clavulanic acid (CA) is a powerful naturally obtained inhibitor for bacterial β-lactamases produced by the organism Streptomyces clavuligerus. Although CA itself can act as an β-lactam antibiotic and is active against a wide spectrum of Gram-positive and Gram-negative bacteria (Mayer & Deckwer, 1996), it is much more effective as a drug in combination with β-lactamase-sensitive penicillins, such as amoxicillin. In that situation, CA protects the β-lactam ring of the amoxicillin from hydrolysis and can maintain its activity against β-lactamase producing bacteria (Bird et al., 1982). The CA potassium salt is widely used as a drug in injectable and solid form, especially combined with amoxicillin sodium and amoxicillin trihydrate (Navarro, 2005).
In this context, an understanding of the structure of CA is important in order to establish its ability to form molecular interactions. Unfortunately, CA is chemically unstable as are the other β-lactam antibiotics, being very sensitive to pH, temperature, and humidity via the hydrolysis degradation mechanism; (Bersanetti et al., 2005; Hickey et al., 2007; Saudagar et al., 2008). The decomposition is also self-catalyzed (Brethauer et al. 2008; Haginaka et al. 1985) and there have been some difficulties in obtaining a single crystals of CA. Therefore, until now there has been no report of a crystal structure of CA. In this study, single crystals of potassium clavulanate were successfully obtained by a low-temperature crystallization process and the crystal structure was determined.
In the molecular structure of potassium clavulanate, Fig. 1, the C5–O2 and C5–O3 distances of 1.262 (5)Å and 1.256 (5) Å, respectively, indicate that the negative charge of the carboxylate group is delocalised. The potassium cation is surrounded by six oxygen atoms, three O2, one O3 and two O4, deriv ed from four different clavulanate anions. The selected bond lengths around the potassium cation are listed in Table 1. These interactions are infinitely linked along the a axis and lead to an ionic (hydrophilic) column structure. These columns are connected by intermolecular O–H···O hydrogen bonds formed between O4-hydroxyl groups and carboxylate-O2 atoms, and form a hydrophobic layer in the ab plane; Fig. 2. By contrast, the remaining hydrophobic groups (i.e. bicyclo groups) form a hydrophobic layer so that the crystal structure comprises alternating hydrophilic and hydrophilic regions.