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BioLiP

Structure of PDB 4kz8 Chain A Binding Site BS01

Receptor Information
>4kz8 Chain A (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 ID1U6
InChIInChI=1S/C8H12N2O2S/c1-3-9-6(11)5-7(12)10(4-2)8(9)13/h3-5H2,1-2H3
InChIKeySHBTUGJAKBRBBJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01S=C1N(C(=O)CC(=O)N1CC)CC
OpenEye OEToolkits 1.7.6CCN1C(=O)CC(=O)N(C1=S)CC
CACTVS 3.370CCN1C(=O)CC(=O)N(CC)C1=S
FormulaC8 H12 N2 O2 S
Name1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione
ChEMBLCHEMBL2136061
DrugBank
ZINCZINC000000119654
PDB chain4kz8 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4kz8 Increasing chemical space coverage by combining empirical and computational fragment screens.
Resolution2.282 Å
Binding residue
(original residue number in PDB)		Y221 A318 T319
Binding residue
(residue number reindexed from 1)		Y218 A315 T316
Annotation score1
Binding affinityMOAD: Ki=1.6mM
PDBbind-CN: -logKd/Ki=2.80,Ki=1.6mM
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:4kz8, PDBe:4kz8, PDBj:4kz8
PDBsum4kz8
PubMed24807704
UniProtP00811|AMPC_ECOLI Beta-lactamase (Gene Name=ampC)

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