Structure of PDB 2cb3 Chain D Binding Site BS02

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 D 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)		H206 T207 H229 R233 W235 N236 Y240 R254 A261 H262 L264 N267 H314 N318 T320 E321 S322
Binding residue
(residue number reindexed from 1)		H33 T34 H56 R60 W62 N63 Y67 R81 A88 H89 L91 N94 H141 N145 T147 E148 S149
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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