Structure of PDB 4okp Chain B Binding Site BS01

Receptor Information
>4okp Chain B (length=358) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQP
VTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNG
ITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANS
SIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGY
REGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQ
LAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITP
PTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAA
WQILNALQ
Ligand information
Ligand ID2V0
InChIInChI=1S/C8H12N2O4S/c1-3-2-15-6(4(9)7(11)12)10-5(3)8(13)14/h4,6,10H,2,9H2,1H3,(H,11,12)(H,13,14)/t4-,6+/m0/s1
InChIKeyWFPVQOKEJDXMTD-UJURSFKZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=C(N[CH](SC1)[CH](N)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6CC1=C(NC(SC1)C(C(=O)O)N)C(=O)O
OpenEye OEToolkits 1.7.6CC1=C(N[C@H](SC1)[C@@H](C(=O)O)N)C(=O)O
CACTVS 3.385CC1=C(N[C@H](SC1)[C@H](N)C(O)=O)C(O)=O
ACDLabs 12.01O=C(O)C(N)C1SCC(=C(C(=O)O)N1)C
FormulaC8 H12 N2 O4 S
Name(2R)-2-[(R)-amino(carboxy)methyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid;
7-aminodeacetoxycephalosporanic acid, hydrolyzed form
ChEMBL
DrugBank
ZINCZINC000103524509
PDB chain4okp Chain B Residue 401 [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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PDB4okp Substrate deconstruction and the nonadditivity of enzyme recognition.
Resolution1.37 Å
Binding residue
(original residue number in PDB)		W93 A160 K164
Binding residue
(residue number reindexed from 1)		W90 A157 K161
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.70,Ki<2mM
Enzymatic activity
Catalytic site (original residue number in PDB) S64 K67 Y112 A114 V121 Y150 G156 E272 K315 A318
Catalytic site (residue number reindexed from 1) S61 K64 Y109 A111 V118 Y147 G153 E269 K312 A315
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4okp, PDBe:4okp, PDBj:4okp
PDBsum4okp
PubMed24791931
UniProtP00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)

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