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Cyclo(Phe1D-Ala2–Gly3–Phe4–APO5) is the minor diastereoisomer of a cyclic penta-peptidomimetic analogue containing a novel 2-amino­propyl lactone (APO) motif, which displays the same number of atoms as the native amino acid glycine and has a methyl group in place of the carbonyl O atom.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S2056989014027406/lh5744sup1.cif
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S2056989014027406/lh5744Isup2.hkl
Contains datablock I

cml

Chemical Markup Language (CML) file https://doi.org/10.1107/S2056989014027406/lh5744Isup3.cml
Supplementary material

CCDC reference: 1039448

Key indicators

  • Single-crystal X-ray study
  • T = 100 K
  • Mean [sigma](C-C) = 0.003 Å
  • R factor = 0.047
  • wR factor = 0.112
  • Data-to-parameter ratio = 12.5

checkCIF/PLATON results

No syntax errors found



Alert level C PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax < 18) ........ 7.14 Note PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.595 3 Report
Alert level G PLAT005_ALERT_5_G No _iucr_refine_instructions_details in the CIF Please Do ! PLAT791_ALERT_4_G The Model has Chirality at C8 ............. S Verify PLAT791_ALERT_4_G The Model has Chirality at C10 ............. R Verify PLAT791_ALERT_4_G The Model has Chirality at C14 ............. S Verify PLAT791_ALERT_4_G The Model has Chirality at C20 ............. R Verify PLAT899_ALERT_4_G SHELXL97 is Deprecated and Succeeded by SHELXL 2014 Note PLAT909_ALERT_3_G Percentage of Observed Data at Theta(Max) still 85 %
0 ALERT level A = Most likely a serious problem - resolve or explain 0 ALERT level B = A potentially serious problem, consider carefully 2 ALERT level C = Check. Ensure it is not caused by an omission or oversight 7 ALERT level G = General information/check it is not something unexpected 0 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 3 ALERT type 3 Indicator that the structure quality may be low 5 ALERT type 4 Improvement, methodology, query or suggestion 1 ALERT type 5 Informative message, check

Computing details top

Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: publCIF (Westrip, 2010).

3,12-Dibenzyl-9,14-dimethyl-1-oxa-4,7,10,13-tetraazacyclopentadecane-2,5,8,11-tetrone top
Crystal data top
C26H32N4O5Dx = 1.360 Mg m3
Mr = 480.56Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, P212121Cell parameters from 9940 reflections
a = 10.126 (9) Åθ = 4.1–68.8°
b = 15.096 (14) ŵ = 0.78 mm1
c = 15.355 (13) ÅT = 100 K
V = 2347 (4) Å3Block, colourless
Z = 40.12 × 0.07 × 0.05 mm
F(000) = 1024
Data collection top
Bruker SMART 6000 CCD
diffractometer
4133 independent reflections
Radiation source: Microstar rotating anode generator3847 reflections with I > 2σ(I)
Incoatec multilayer mirrors monochromatorRint = 0.075
Detector resolution: 5.6 pixels mm-1θmax = 66.6°, θmin = 4.1°
ω scansh = 1212
Absorption correction: multi-scan
(SADABS; Sheldrick, 1999)
k = 1717
Tmin = 0.486, Tmax = 0.753l = 1818
23011 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.047H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.112 w = 1/[σ2(Fo2) + (0.0764P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.011
4133 reflectionsΔρmax = 0.31 e Å3
330 parametersΔρmin = 0.43 e Å3
0 restraintsAbsolute structure: Flack x determined using 1590 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons & Flack, 2004)
0 constraintsAbsolute structure parameter: 0.10 (11)
Primary atom site location: structure-invariant direct methods
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.6916 (2)0.75967 (14)0.68262 (14)0.0209 (4)
H10.68940.73330.73880.025*
C20.6031 (2)0.82691 (14)0.66282 (14)0.0227 (4)
H20.54310.84750.70580.027*
C30.6026 (2)0.86397 (14)0.58022 (15)0.0223 (4)
H30.54130.90950.56630.027*
C40.6915 (2)0.83465 (15)0.51801 (14)0.0231 (4)
H40.69040.85940.46110.028*
C50.7827 (2)0.76883 (14)0.53901 (13)0.0206 (4)
H50.84500.75010.49660.025*
C60.7835 (2)0.73002 (14)0.62175 (13)0.0191 (4)
C70.8833 (2)0.65948 (13)0.64407 (13)0.0191 (4)
H7A0.92030.63540.58930.023*
H7B0.83740.61050.67440.023*
C80.9979 (2)0.69186 (13)0.70179 (13)0.0178 (4)
H81.03990.74480.67410.021*
N91.09594 (18)0.62140 (11)0.70982 (11)0.0188 (4)
H91.056 (2)0.5716 (19)0.7369 (18)0.023*
C101.2144 (2)0.64565 (14)0.76043 (13)0.0196 (4)
H101.19090.69410.80210.024*
C111.2647 (2)0.56634 (14)0.81143 (14)0.0213 (4)
H11A1.26320.51300.77390.026*
H11B1.35710.57700.82970.026*
O121.18248 (15)0.55144 (9)0.88820 (9)0.0204 (3)
C131.0956 (2)0.48517 (13)0.88625 (14)0.0196 (4)
C141.0182 (2)0.48060 (14)0.97123 (13)0.0198 (4)
H141.07800.45361.01580.024*
N150.98462 (18)0.56809 (12)1.00179 (11)0.0191 (4)
H150.949 (3)0.6021 (18)0.9664 (19)0.023*
C161.0227 (2)0.59836 (14)1.08029 (13)0.0184 (4)
C170.9816 (2)0.69272 (14)1.10269 (13)0.0212 (4)
H17A0.92360.69041.15450.025*
H17B1.06190.72611.11940.025*
N180.9139 (2)0.74228 (11)1.03547 (11)0.0197 (4)
H180.828 (3)0.7378 (18)1.0336 (17)0.024*
C190.9831 (2)0.77969 (13)0.96966 (13)0.0175 (4)
C200.8968 (2)0.82801 (14)0.90145 (13)0.0197 (4)
H200.80260.80970.90900.024*
N210.94164 (18)0.80253 (12)0.81497 (12)0.0188 (4)
H210.953 (3)0.8414 (19)0.7802 (19)0.023*
C220.94722 (18)0.71732 (13)0.79294 (13)0.0165 (4)
O230.91694 (15)0.65798 (9)0.84460 (9)0.0196 (3)
C241.3230 (2)0.67838 (15)0.69969 (15)0.0236 (5)
H24A1.35040.63010.66100.035*
H24B1.39880.69820.73420.035*
H24C1.28960.72790.66470.035*
O251.08111 (16)0.43461 (10)0.82577 (10)0.0245 (3)
C260.8961 (2)0.42006 (14)0.96385 (15)0.0238 (5)
H26A0.92450.36090.94340.029*
H26B0.85630.41281.02230.029*
C270.7928 (2)0.45570 (14)0.90239 (15)0.0222 (5)
C280.7071 (2)0.52271 (15)0.92819 (15)0.0244 (5)
H280.70780.54260.98690.029*
C290.6201 (2)0.56087 (15)0.86874 (17)0.0275 (5)
H290.56310.60720.88720.033*
C300.6156 (2)0.53217 (15)0.78319 (16)0.0271 (5)
H300.55680.55900.74280.033*
C310.6983 (2)0.46364 (15)0.75708 (15)0.0254 (5)
H310.69500.44260.69880.030*
C320.7853 (2)0.42612 (15)0.81573 (15)0.0245 (5)
H320.84130.37930.79710.029*
O331.08418 (17)0.55439 (10)1.13399 (10)0.0268 (4)
O341.10326 (14)0.77972 (10)0.96627 (9)0.0220 (3)
C350.9080 (3)0.92754 (14)0.91424 (15)0.0258 (5)
H35A1.00020.94580.90670.039*
H35B0.87830.94310.97300.039*
H35C0.85270.95790.87120.039*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0215 (10)0.0231 (10)0.0180 (10)0.0008 (9)0.0012 (8)0.0021 (8)
C20.0219 (10)0.0258 (10)0.0206 (11)0.0004 (9)0.0018 (8)0.0027 (8)
C30.0211 (10)0.0214 (10)0.0244 (11)0.0019 (9)0.0031 (9)0.0020 (8)
C40.0258 (11)0.0238 (10)0.0197 (10)0.0018 (9)0.0035 (9)0.0019 (9)
C50.0214 (11)0.0239 (11)0.0163 (10)0.0001 (8)0.0017 (8)0.0022 (8)
C60.0191 (10)0.0199 (10)0.0183 (10)0.0038 (8)0.0030 (8)0.0015 (8)
C70.0221 (10)0.0192 (10)0.0160 (9)0.0009 (8)0.0005 (8)0.0017 (8)
C80.0202 (10)0.0172 (9)0.0161 (9)0.0002 (8)0.0009 (8)0.0029 (7)
N90.0199 (9)0.0186 (9)0.0180 (9)0.0007 (7)0.0003 (7)0.0003 (7)
C100.0206 (11)0.0209 (10)0.0174 (10)0.0004 (8)0.0006 (8)0.0028 (8)
C110.0191 (10)0.0262 (11)0.0186 (10)0.0001 (8)0.0023 (8)0.0007 (9)
O120.0213 (7)0.0245 (8)0.0153 (7)0.0021 (6)0.0003 (6)0.0002 (6)
C130.0207 (10)0.0161 (9)0.0221 (10)0.0023 (8)0.0013 (8)0.0006 (8)
C140.0248 (11)0.0190 (10)0.0157 (9)0.0008 (9)0.0005 (8)0.0021 (8)
N150.0253 (9)0.0165 (8)0.0155 (9)0.0030 (7)0.0023 (7)0.0015 (7)
C160.0187 (10)0.0229 (10)0.0137 (9)0.0011 (8)0.0009 (8)0.0029 (8)
C170.0284 (11)0.0204 (10)0.0148 (10)0.0001 (9)0.0004 (9)0.0001 (7)
N180.0205 (9)0.0203 (9)0.0183 (9)0.0002 (7)0.0008 (7)0.0006 (7)
C190.0228 (11)0.0151 (9)0.0145 (9)0.0016 (8)0.0000 (8)0.0030 (7)
C200.0217 (10)0.0193 (10)0.0182 (10)0.0019 (9)0.0007 (8)0.0003 (8)
N210.0260 (9)0.0169 (9)0.0134 (8)0.0004 (7)0.0001 (7)0.0023 (7)
C220.0154 (9)0.0188 (10)0.0153 (10)0.0001 (7)0.0038 (7)0.0012 (8)
O230.0240 (7)0.0194 (7)0.0153 (7)0.0010 (6)0.0002 (6)0.0011 (5)
C240.0233 (10)0.0239 (10)0.0237 (11)0.0002 (9)0.0006 (9)0.0003 (8)
O250.0272 (8)0.0244 (7)0.0219 (8)0.0005 (7)0.0011 (6)0.0057 (6)
C260.0273 (11)0.0189 (10)0.0251 (11)0.0004 (9)0.0024 (9)0.0027 (8)
C270.0200 (10)0.0173 (10)0.0294 (11)0.0052 (8)0.0027 (9)0.0024 (8)
C280.0225 (11)0.0234 (10)0.0273 (11)0.0047 (9)0.0041 (9)0.0040 (9)
C290.0189 (11)0.0236 (11)0.0399 (14)0.0003 (9)0.0004 (9)0.0027 (10)
C300.0207 (10)0.0233 (11)0.0374 (13)0.0024 (9)0.0028 (9)0.0022 (10)
C310.0220 (11)0.0266 (11)0.0275 (12)0.0054 (9)0.0004 (9)0.0038 (9)
C320.0220 (11)0.0205 (10)0.0309 (11)0.0016 (9)0.0025 (9)0.0034 (9)
O330.0357 (9)0.0265 (8)0.0183 (7)0.0055 (7)0.0044 (7)0.0016 (6)
O340.0221 (8)0.0232 (7)0.0206 (7)0.0003 (6)0.0016 (6)0.0003 (6)
C350.0357 (12)0.0195 (10)0.0221 (10)0.0034 (10)0.0016 (9)0.0014 (8)
Geometric parameters (Å, º) top
C1—C21.387 (3)C16—C171.523 (3)
C1—C61.393 (3)C17—N181.447 (3)
C1—H10.9500C17—H17A0.9900
C2—C31.386 (3)C17—H17B0.9900
C2—H20.9500N18—C191.353 (3)
C3—C41.385 (3)N18—H180.87 (3)
C3—H30.9500C19—O341.218 (3)
C4—C51.394 (3)C19—C201.546 (3)
C4—H40.9500C20—N211.455 (3)
C5—C61.399 (3)C20—C351.519 (3)
C5—H50.9500C20—H201.0000
C6—C71.507 (3)N21—C221.331 (3)
C7—C81.540 (3)N21—H210.80 (3)
C7—H7A0.9900C22—O231.235 (3)
C7—H7B0.9900C24—H24A0.9800
C8—N91.460 (3)C24—H24B0.9800
C8—C221.539 (3)C24—H24C0.9800
C8—H81.0000C26—C271.508 (3)
N9—C101.475 (3)C26—H26A0.9900
N9—H90.95 (3)C26—H26B0.9900
C10—C111.519 (3)C27—C281.391 (3)
C10—C241.524 (3)C27—C321.406 (4)
C10—H101.0000C28—C291.393 (4)
C11—O121.461 (3)C28—H280.9500
C11—H11A0.9900C29—C301.384 (4)
C11—H11B0.9900C29—H290.9500
O12—C131.333 (3)C30—C311.390 (4)
C13—O251.211 (3)C30—H300.9500
C13—C141.523 (3)C31—C321.381 (4)
C14—N151.442 (3)C31—H310.9500
C14—C261.542 (3)C32—H320.9500
C14—H141.0000C35—H35A0.9800
N15—C161.345 (3)C35—H35B0.9800
N15—H150.83 (3)C35—H35C0.9800
C16—O331.228 (3)
C2—C1—C6121.3 (2)N18—C17—C16116.85 (18)
C2—C1—H1119.4N18—C17—H17A108.1
C6—C1—H1119.4C16—C17—H17A108.1
C3—C2—C1119.9 (2)N18—C17—H17B108.1
C3—C2—H2120.1C16—C17—H17B108.1
C1—C2—H2120.1H17A—C17—H17B107.3
C4—C3—C2120.0 (2)C19—N18—C17120.2 (2)
C4—C3—H3120.0C19—N18—H18121.6 (18)
C2—C3—H3120.0C17—N18—H18117.1 (18)
C3—C4—C5119.9 (2)O34—C19—N18123.31 (19)
C3—C4—H4120.0O34—C19—C20122.35 (19)
C5—C4—H4120.0N18—C19—C20114.24 (19)
C4—C5—C6120.81 (19)N21—C20—C35110.87 (18)
C4—C5—H5119.6N21—C20—C19108.49 (17)
C6—C5—H5119.6C35—C20—C19109.68 (18)
C1—C6—C5118.1 (2)N21—C20—H20109.3
C1—C6—C7121.49 (19)C35—C20—H20109.3
C5—C6—C7120.40 (18)C19—C20—H20109.3
C6—C7—C8114.32 (17)C22—N21—C20120.04 (18)
C6—C7—H7A108.7C22—N21—H21122.1 (19)
C8—C7—H7A108.7C20—N21—H21117.4 (19)
C6—C7—H7B108.7O23—C22—N21121.80 (19)
C8—C7—H7B108.7O23—C22—C8119.05 (18)
H7A—C7—H7B107.6N21—C22—C8119.11 (18)
N9—C8—C22109.38 (16)C10—C24—H24A109.5
N9—C8—C7109.26 (17)C10—C24—H24B109.5
C22—C8—C7110.56 (17)H24A—C24—H24B109.5
N9—C8—H8109.2C10—C24—H24C109.5
C22—C8—H8109.2H24A—C24—H24C109.5
C7—C8—H8109.2H24B—C24—H24C109.5
C8—N9—C10114.60 (16)C27—C26—C14113.00 (18)
C8—N9—H9109.2 (15)C27—C26—H26A109.0
C10—N9—H9107.9 (15)C14—C26—H26A109.0
N9—C10—C11110.42 (17)C27—C26—H26B109.0
N9—C10—C24110.16 (18)C14—C26—H26B109.0
C11—C10—C24109.20 (18)H26A—C26—H26B107.8
N9—C10—H10109.0C28—C27—C32117.8 (2)
C11—C10—H10109.0C28—C27—C26120.9 (2)
C24—C10—H10109.0C32—C27—C26121.1 (2)
O12—C11—C10110.26 (17)C27—C28—C29120.6 (2)
O12—C11—H11A109.6C27—C28—H28119.7
C10—C11—H11A109.6C29—C28—H28119.7
O12—C11—H11B109.6C30—C29—C28120.9 (2)
C10—C11—H11B109.6C30—C29—H29119.6
H11A—C11—H11B108.1C28—C29—H29119.6
C13—O12—C11118.28 (16)C29—C30—C31119.2 (2)
O25—C13—O12124.8 (2)C29—C30—H30120.4
O25—C13—C14124.47 (19)C31—C30—H30120.4
O12—C13—C14110.74 (17)C32—C31—C30120.1 (2)
N15—C14—C13111.01 (17)C32—C31—H31120.0
N15—C14—C26112.16 (19)C30—C31—H31120.0
C13—C14—C26112.10 (18)C31—C32—C27121.4 (2)
N15—C14—H14107.1C31—C32—H32119.3
C13—C14—H14107.1C27—C32—H32119.3
C26—C14—H14107.1C20—C35—H35A109.5
C16—N15—C14122.33 (19)C20—C35—H35B109.5
C16—N15—H15120.0 (18)H35A—C35—H35B109.5
C14—N15—H15117.2 (18)C20—C35—H35C109.5
O33—C16—N15124.3 (2)H35A—C35—H35C109.5
O33—C16—C17119.49 (19)H35B—C35—H35C109.5
N15—C16—C17116.21 (18)
C6—C1—C2—C32.0 (3)O33—C16—C17—N18177.65 (19)
C1—C2—C3—C40.9 (3)N15—C16—C17—N184.0 (3)
C2—C3—C4—C51.0 (3)C16—C17—N18—C1979.0 (3)
C3—C4—C5—C61.7 (3)C17—N18—C19—O345.5 (3)
C2—C1—C6—C51.2 (3)C17—N18—C19—C20178.25 (17)
C2—C1—C6—C7177.58 (19)O34—C19—C20—N2149.5 (3)
C4—C5—C6—C10.6 (3)N18—C19—C20—N21134.16 (19)
C4—C5—C6—C7179.45 (19)O34—C19—C20—C3571.7 (3)
C1—C6—C7—C875.1 (3)N18—C19—C20—C35104.6 (2)
C5—C6—C7—C8103.7 (2)C35—C20—N21—C22175.89 (19)
C6—C7—C8—N9172.90 (16)C19—C20—N21—C2255.4 (2)
C6—C7—C8—C2266.7 (2)C20—N21—C22—O231.1 (3)
C22—C8—N9—C1061.6 (2)C20—N21—C22—C8178.64 (17)
C7—C8—N9—C10177.27 (17)N9—C8—C22—O2345.8 (2)
C8—N9—C10—C11145.33 (18)C7—C8—C22—O2374.5 (2)
C8—N9—C10—C2494.0 (2)N9—C8—C22—N21131.84 (19)
N9—C10—C11—O1277.0 (2)C7—C8—C22—N21107.8 (2)
C24—C10—C11—O12161.69 (17)N15—C14—C26—C2759.4 (2)
C10—C11—O12—C13103.6 (2)C13—C14—C26—C2766.3 (2)
C11—O12—C13—O251.6 (3)C14—C26—C27—C2878.9 (3)
C11—O12—C13—C14179.37 (16)C14—C26—C27—C3297.2 (2)
O25—C13—C14—N15140.7 (2)C32—C27—C28—C292.1 (3)
O12—C13—C14—N1540.3 (2)C26—C27—C28—C29174.1 (2)
O25—C13—C14—C2614.4 (3)C27—C28—C29—C301.0 (3)
O12—C13—C14—C26166.61 (17)C28—C29—C30—C310.7 (3)
C13—C14—N15—C16121.6 (2)C29—C30—C31—C321.2 (3)
C26—C14—N15—C16112.1 (2)C30—C31—C32—C270.0 (3)
C14—N15—C16—O332.8 (3)C28—C27—C32—C311.7 (3)
C14—N15—C16—C17178.95 (19)C26—C27—C32—C31174.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N9—H9···O250.95 (3)2.49 (3)3.338 (3)149 (2)
N15—H15···O230.83 (3)2.08 (3)2.853 (3)155 (2)
N18—H18···O34i0.87 (3)2.29 (3)3.163 (4)177 (3)
N21—H21···O25ii0.80 (3)2.18 (3)2.949 (3)161 (3)
Symmetry codes: (i) x1/2, y+3/2, z+2; (ii) x+2, y+1/2, z+3/2.
Selected backbone torsion angles (°) top
Phe1C10—N9—C8—C22φ1-61.6 (2)
Phe1N9—C8—C22—N21ψ1131.8 (2)
D-Ala2C22—N21—C20—C19φ255.4 (2)
D-Ala2N21—C20—C19—N18ψ2-134.2 (2)
Gly3C19—N18—C17—C16φ3-79.0 (3)
Gly3N18—C17—C16—N15ψ3-4.0 (3)
Phe4C16—N15—C14—C13φ4-121.6 (2)
Phe4N15—C14—C13—O12ψ440.3 (2)
APO5C13—O12—C11—C10φ5103.6 (2)
APO5O12—C11—C10—N9ψ5-77.0 (2)
 

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