Structure of PDB 6d1d Chain A Binding Site BS03

Receptor Information
>6d1d 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 IDGTV
InChIInChI=1S/C12H13O5P/c1-7-3-8(2)12-9(6-18(14,15)16)5-11(13)17-10(12)4-7/h3-5H,6H2,1-2H3,(H2,14,15,16)
InChIKeyAPYPWKQCSUQQTA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cc(C)c2C(=CC(=O)Oc2c1)C[P](O)(O)=O
ACDLabs 12.01Cc2cc(C)c1C(CP(O)(O)=O)=CC(=O)Oc1c2
OpenEye OEToolkits 2.0.6Cc1cc(c2c(c1)OC(=O)C=C2CP(=O)(O)O)C
FormulaC12 H13 O5 P
Name[(5,7-dimethyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid
ChEMBLCHEMBL4545793
DrugBank
ZINCZINC000020760687
PDB chain6d1d 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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PDB6d1d Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		H122 D124 H189 C208 N220
Binding residue
(residue number reindexed from 1)		H81 D83 H148 C167 N179
Annotation score1
Binding affinityMOAD: Ki=33.8uM
PDBbind-CN: -logKd/Ki=4.47,Ki=33.8uM
BindingDB: Ki=100000nM
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:6d1d, PDBe:6d1d, PDBj:6d1d
PDBsum6d1d
PubMed31483651
UniProtC7C422|BLAN1_KLEPN Metallo-beta-lactamase type 2 (Gene Name=blaNDM-1)

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