Structure of PDB 5zj2 Chain A Binding Site BS03

Receptor Information
>5zj2 Chain A (length=229) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDT
AWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYA
NALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTS
DNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFP
KASMIVMSHSAPDSRAAITHTARMADKLR
Ligand information
Ligand IDMCO
InChIInChI=1S/C9H15NO3S/c1-6(5-14)8(11)10-4-2-3-7(10)9(12)13/h6-7,14H,2-5H2,1H3,(H,12,13)/t6-,7-/m1/s1
InChIKeyFAKRSMQSSFJEIM-RNFRBKRXSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C1N(C(=O)C(C)CS)CCC1
CACTVS 3.385C[CH](CS)C(=O)N1CCC[CH]1C(O)=O
CACTVS 3.385C[C@H](CS)C(=O)N1CCC[C@@H]1C(O)=O
OpenEye OEToolkits 1.7.5CC(CS)C(=O)N1CCCC1C(=O)O
OpenEye OEToolkits 1.7.5C[C@H](CS)C(=O)N1CCC[C@@H]1C(=O)O
FormulaC9 H15 N O3 S
Name1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
ChEMBLCHEMBL434965
DrugBank
ZINCZINC000000020226
PDB chain5zj2 Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5zj2 Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors
Resolution1.1 Å
Binding residue
(original residue number in PDB)		M67 V73 W93 H122 D124 H189 G219 N220 H250
Binding residue
(residue number reindexed from 1)		M26 V32 W52 H81 D83 H148 G178 N179 H209
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H120 H122 D124 H189 C208 K211 N220 H250
Catalytic site (residue number reindexed from 1) H79 H81 D83 H148 C167 K170 N179 H209
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5zj2, PDBe:5zj2, PDBj:5zj2
PDBsum5zj2
PubMed
UniProtC7C422|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)

[Back to BioLiP]