Structure of PDB 2cb3 Chain D Binding Site BS01

Receptor Information
>2cb3 Chain D (length=170) Species: 7227 (Drosophila melanogaster) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSAIIPRSSWLAQKPMDEPLPLQLPVKYVVILHTATESSEKRAINVRLIR
DMQSFHIESRGWNDIAYNFLVGCDGNIYEGRGWKTVGAHTLGYNRISLGI
SFIGCFMKELPTADALNMCRNLLARGVEDGHISTDYRLICHCQCNSTESP
GRRLYEEIQTWPHFYNIEEE
Ligand information
Ligand IDMLD
InChIInChI=1S/C37H59N7O20/c1-13(30(51)44-20(35(58)59)9-10-23(48)43-19(8-6-7-18(38)34(56)57)32(53)40-14(2)33(54)55)39-31(52)15(3)61-29-25(42-17(5)47)36-60-12-22(63-36)28(29)64-37-24(41-16(4)46)27(50)26(49)21(11-45)62-37/h13-15,18-22,24-29,36-37,45,49-50H,6-12,38H2,1-5H3,(H,39,52)(H,40,53)(H,41,46)(H,42,47)(H,43,48)(H,44,51)(H,54,55)(H,56,57)(H,58,59)/t13-,14+,15+,18+,19-,20+,21+,22+,24+,25+,26+,27+,28+,29+,36+,37-/m0/s1
InChIKeyUPFMKPIBAIPLHT-RSJSDIDPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O)O)N)C(=O)N[C@H](C)C(=O)O)C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@@H]2OC[C@H]([C@H]1O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)NC(=O)C)O2)NC(=O)C
OpenEye OEToolkits 1.5.0CC(C(=O)NC(CCC(=O)NC(CCCC(C(=O)O)N)C(=O)NC(C)C(=O)O)C(=O)O)NC(=O)C(C)OC1C(C2OCC(C1OC3C(C(C(C(O3)CO)O)O)NC(=O)C)O2)NC(=O)C
ACDLabs 10.04O=C(O)C(NC(=O)C(NC(=O)CCC(C(=O)O)NC(=O)C(NC(=O)C(OC3C(OC1OC(CO)C(O)C(O)C1NC(=O)C)C2OC(OC2)C3NC(=O)C)C)C)CCCC(C(=O)O)N)C
CACTVS 3.341C[CH](NC(=O)[CH](CCC[CH](N)C(O)=O)NC(=O)CC[CH](NC(=O)[CH](C)NC(=O)[CH](C)O[CH]1[CH](NC(C)=O)[CH]2OC[CH](O2)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3NC(C)=O)C(O)=O)C(O)=O
CACTVS 3.341C[C@@H](NC(=O)[C@H](CCC[C@@H](N)C(O)=O)NC(=O)CC[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H](C)O[C@@H]1[C@@H](NC(C)=O)[C@@H]2OC[C@@H](O2)[C@H]1O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3NC(C)=O)C(O)=O)C(O)=O
FormulaC37 H59 N7 O20
NameGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA;
2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE
ChEMBL
DrugBankDB04736
ZINCZINC000096006131
PDB chain2cb3 Chain B Residue 1344 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2cb3 Structural Basis for Preferential Recognition of Diaminopimelic Acid-Type Peptidoglycan by a Subset of Peptidoglycan Recognition Proteins
Resolution2.4 Å
Binding residue
(original residue number in PDB)		R223 E231
Binding residue
(residue number reindexed from 1)		R50 E58
Annotation score1
Binding affinityMOAD: Kd=27nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y240
Catalytic site (residue number reindexed from 1) Y67
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008745 N-acetylmuramoyl-L-alanine amidase activity
GO:0042834 peptidoglycan binding
Biological Process
GO:0009253 peptidoglycan catabolic process
GO:0045087 innate immune response

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2cb3, PDBe:2cb3, PDBj:2cb3
PDBsum2cb3
PubMed16428381
UniProtQ9VXN9|PGPLE_DROME Peptidoglycan-recognition protein LE (Gene Name=PGRP-LE)

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