Structure of PDB 6d1g Chain A Binding Site BS03

Receptor Information
>6d1g 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 IDYKG
InChIInChI=1S/C11H10BrO5P/c1-6-2-8(12)11-7(5-18(14,15)16)4-10(13)17-9(11)3-6/h2-4H,5H2,1H3,(H2,14,15,16)
InChIKeyAVDUOTYJUPESMO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc2c(c(c1)Br)C(=CC(=O)O2)CP(=O)(O)O
ACDLabs 12.01Cc2cc(Br)c1C(CP(=O)(O)O)=CC(=O)Oc1c2
CACTVS 3.385Cc1cc(Br)c2C(=CC(=O)Oc2c1)C[P](O)(O)=O
FormulaC11 H10 Br O5 P
Name[(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid
ChEMBLCHEMBL4519591
DrugBank
ZINCZINC000621485606
PDB chain6d1g Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6d1g Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Resolution1.15 Å
Binding residue
(original residue number in PDB)		M67 V73 H122 D124 H189 C208 N220 H250
Binding residue
(residue number reindexed from 1)		M26 V32 H81 D83 H148 C167 N179 H209
Annotation score1
Binding affinityMOAD: Ki=34.2uM
PDBbind-CN: -logKd/Ki=4.47,Ki=34.2uM
BindingDB: Ki=54970nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6d1g, PDBe:6d1g, PDBj:6d1g
PDBsum6d1g
PubMed31483651
UniProtC7C422|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)

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