Structure of PDB 5hlb Chain A Binding Site BS01

Receptor Information
>5hlb Chain A (length=733) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WLLLKLAIVFAVLIAIYGVYLDQKIRSRIDGKVWQLPAAVYGRMVNLEPD
MTISKNEMVKLLEATQYRQVSKMTRPGEFTVQANSIEMIRRPFDFPDSKE
GQVRARLTFDGDHLATIVNMENNRQFGFFRLDPRLITMISSPNGEQRLFV
PRSGFPDLLVDTLLATEDRHFYEHDGISLYSIGRAVLANLTAGRTVQGAS
TLTQQLVKNLFLSSERSYWRKANEAYMALIMDARYSKDRILELYMNEVYL
GQSGDNEIRGFPLASLYYFGRPVEELSLDQQALLVGMVKGASIYNPWRNP
KLALERRNLVLRLLQQQQIIDQELYDMLSARPLGVQPRGGVISPQPAFMQ
LVRQELQAKLGDKVKDLSGVKIFTTFDSVAQDAAEKAAVEGIPALKKQRK
LSDLETAIVVVDRFSGEVRAMVGGSEPQFAGYNRAMQARRSIGSLAKPAT
YLTALSQPKIYRLNTWIADAPIALRQPNGQVWSPQNDDRRYSESGRVMLV
DALTRSMNVPTVNLGMALGLPAVTETWIKLGVPKDQLHPVPAMLLGALNL
TPIEVAQAFQTIASGGNRAPLSALRSVIAEDGKVLYQSFPQAERAVPAQA
AYLTLWTMQQVVQRGTGRQLGAKYPNLHLAGKTGTTNNNVDTWFAGIDGS
TVTITWVGRDNNQPTKLYGASGAMSIYQRYLANQTPTPLNLVPPEDIADM
GVDYDGNFVCSGGMRILPVWTSDPQSLCQQSEM
Ligand information
Ligand IDM0E
InChIInChI=1S/C69H106N5O34P/c1-30(2)15-14-17-31(3)18-19-33(5)22-25-68(9,10)24-13-12-16-32(4)23-26-96-41(61(90)91)29-98-109(94,95)108-66-56(57(107-67(71)92)69(11,93)58(106-66)59(70)88)105-63-44(73-36(8)77)47(82)54(40(101-63)28-97-64-51(86)48(83)45(80)39(27-75)100-64)103-62-43(72-35(7)76)46(81)53(34(6)99-62)102-65-52(87)49(84)50(85)55(104-65)60(89)74-42-37(78)20-21-38(42)79/h13,15,18,20-21,23-24,34,39-41,43-58,62-66,75,80-87,93H,5,12,14,16-17,19,22,25-29H2,1-4,6-11H3,(H2,70,88)(H2,71,92)(H,72,76)(H,73,77)(H,90,91)(H,94,95)(H2,74,78,79,89)/t34-,39-,40-,41-,43-,44-,45-,46-,47-,48+,49+,50-,51-,52-,53-,54-,55+,56-,57-,58-,62+,63+,64-,65-,66-,69+/m1/s1
InChIKeyNXPRJQIAIORCGO-ZLPAOQQDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OC2C(OC(C(C2O)NC(=O)C)OC3C(C(C(OC3OP(=O)(O)OCC(C(=O)O)OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(=O)N)(C)O)OC(=O)N)COC4C(C(C(C(O4)CO)O)O)O)NC(=O)C)O)OC5C(C(C(C(O5)C(=O)NC6=C(C=CC6=O)O)O)O)O
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](O[C@H]([C@@H]([C@H]2O)NC(=O)C)O[C@@H]3[C@H]([C@]([C@H](O[C@@H]3O[P@@](=O)(O)OC[C@H](C(=O)O)OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(=O)N)(C)O)OC(=O)N)CO[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)NC(=O)C)O)O[C@H]5[C@@H]([C@H]([C@H]([C@H](O5)C(=O)NC6=C(C=CC6=O)O)O)O)O
CACTVS 3.341C[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](NC(C)=O)[C@@H](O[C@@H]2CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O[C@H]4[C@H](O[C@H](C(N)=O)[C@@](C)(O)[C@@H]4OC(N)=O)O[P@](O)(=O)OC[C@@H](OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(O)=O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1O[C@@H]5O[C@@H]([C@H](O)[C@H](O)[C@H]5O)C(=O)NC6=C(O)C=CC6=O
ACDLabs 10.04O=C(NC1=C(O)C=CC1=O)C6OC(OC2C(O)C(NC(=O)C)C(OC2C)OC4C(OC(OC3C(OC(=O)N)C(O)(C)C(OC3OP(=O)(O)OCC(OC\C=C(/C)CC/C=C/C(C)(C)CCC(=C)/C\C=C(/C)CC\C=C(/C)C)C(=O)O)C(=O)N)C(NC(=O)C)C4O)COC5OC(C(O)C(O)C5O)CO)C(O)C(O)C6O
CACTVS 3.341C[CH]1O[CH](O[CH]2[CH](O)[CH](NC(C)=O)[CH](O[CH]2CO[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3O)O[CH]4[CH](O[CH](C(N)=O)[C](C)(O)[CH]4OC(N)=O)O[P](O)(=O)OC[CH](OCC=C(C)CCC=CC(C)(C)CCC(=C)CC=C(C)CCC=C(C)C)C(O)=O)[CH](NC(C)=O)[CH](O)[CH]1O[CH]5O[CH]([CH](O)[CH](O)[CH]5O)C(=O)NC6=C(O)C=CC6=O
FormulaC69 H106 N5 O34 P
NameMOENOMYCIN;
MOENOMYCIN
ChEMBL
DrugBank
ZINC
PDB chain5hlb Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5hlb Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition.
Resolution2.42 Å
Binding residue
(original residue number in PDB)		G264 Q271 K274 N275 R286 Y315 E323 V354 K355 G356 S358 I359
Binding residue
(residue number reindexed from 1)		G198 Q205 K208 N209 R220 Y249 E257 V288 K289 G290 S292 I293
Annotation score1
Binding affinityMOAD: ic50=64.3nM
Enzymatic activity
Enzyme Commision number 2.4.99.28: peptidoglycan glycosyltransferase.
3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
GO:0008658 penicillin binding
GO:0008955 peptidoglycan glycosyltransferase activity
Biological Process
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
Cellular Component
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5hlb, PDBe:5hlb, PDBj:5hlb
PDBsum5hlb
PubMed27899450
UniProtP02919|PBPB_ECOLI Penicillin-binding protein 1B (Gene Name=mrcB)

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