Structure of PDB 1p6d Chain A Binding Site BS04

Receptor Information
>1p6d Chain A (length=245) Species: 1396 (Bacillus cereus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WSAEDKHKEGVNSHLWIVNRAIDIMSRNTTLVKQDRVAQLNEWRTELENG
IYAANYENPYYDNSTFASHFYDPDNGKTYIPFAKQAKETGAKYFKLAGES
YKNKDMKQAFFYLGLSLHYLGDVNQPMHAANFTNLSYPQGFHSKYENFVD
TIKDNYKVTDGNGYWNWKGTNPEEWIHGAAVVAKQDYSGIVNDNTKDWFV
KAAVSQEYADKWRAEVTPMTGKRLMDAQRVTAGYIQLWFDTYGDR
Ligand information
Ligand ID3PC
InChIInChI=1S/C21H42NO7P/c1-6-8-10-12-20(23)27-18-19(29-21(24)13-11-9-7-2)14-17-30(25,26)28-16-15-22(3,4)5/h19H,6-18H2,1-5H3/t19-/m0/s1
InChIKeyBRTDPJPTKQNAET-IBGZPJMESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCC(=O)OC[C@H](CC[P]([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCCCC
ACDLabs 10.04O=P([O-])(OCC[N+](C)(C)C)CCC(OC(=O)CCCCC)COC(=O)CCCCC
OpenEye OEToolkits 1.7.5CCCCCC(=O)OCC(CCP(=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCC
OpenEye OEToolkits 1.7.5CCCCCC(=O)OC[C@H](CCP(=O)([O-])OCC[N+](C)(C)C)OC(=O)CCCCC
CACTVS 3.385CCCCCC(=O)OC[CH](CC[P]([O-])(=O)OCC[N+](C)(C)C)OC(=O)CCCCC
FormulaC21 H42 N O7 P
Name(3S)-3,4-DI-N-HEXANOYLOXYBUTYL-1-PHOSPHOCHOLINE
ChEMBL
DrugBankDB03827
ZINC
PDB chain1p6d Chain A Residue 601 [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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PDB1p6d Using X-ray crystallography of the Asp55Asn mutant of the phosphatidylcholine-preferring phospholipase C from Bacillus cereus to support the mechanistic role of Asp55 as the general base.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		W1 E4 N55 F66 H118 D122 H128 T133 N134 E146
Binding residue
(residue number reindexed from 1)		W1 E4 N55 F66 H118 D122 H128 T133 N134 E146
Annotation score1
Binding affinityMOAD: Ki=1.15mM
PDBbind-CN: -logKd/Ki=2.94,Ki=1.15mM
Enzymatic activity
Catalytic site (original residue number in PDB) H14 N55 H69 H118 D122 H128 H142 E146
Catalytic site (residue number reindexed from 1) H14 N55 H69 H118 D122 H128 H142 E146
Enzyme Commision number 3.1.4.3: phospholipase C.
Gene Ontology
Molecular Function
GO:0004629 phospholipase C activity
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016788 hydrolase activity, acting on ester bonds
GO:0034480 phosphatidylcholine phospholipase C activity
GO:0046872 metal ion binding
Biological Process
GO:0031640 killing of cells of another organism

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1p6d, PDBe:1p6d, PDBj:1p6d
PDBsum1p6d
PubMed12921783
UniProtP09598|PHLC_BACCE Phospholipase C (Gene Name=plc)

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