Structure of PDB 6dd1 Chain A Binding Site BS03

Receptor Information

>6dd1 Chain A (length=231) Species: 287 (Pseudomonas aeruginosa)

EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELL
LIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGV
ATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHST
DNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYP
EAQFVIPGHGLPGGLDLLKHTTNVVKAHTNR

Ligand information

• Ligand ID: M3Q
• InChI: InChI=1S/C10H10NO3P/c12-15(13,14)7-9-4-1-3-8-5-2-6-11-10(8)9/h1-6H,7H2,(H2,12,13,14)
• InChIKey: JEAIVEQRSHHAIR-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: O[P](O)(=O)Cc1cccc2cccnc12
  OpenEye OEToolkits 2.0.6: c1cc2cccnc2c(c1)CP(=O)(O)O
  ACDLabs 12.01: C(c1cccc2cccnc12)P(O)(=O)O
• Formula: C10 H10 N O3 P
• Name: [(quinolin-8-yl)methyl]phosphonic acid
• ChEMBL: CHEMBL4472640
• ZINC: ZINC000039256456
• PDB chain: 6dd1 Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dd1 Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F61 W87 H118 D120 H196 N233
• Binding residue (residue number reindexed from 1): F31 W56 H85 D87 H148 N179
• Annotation score: 1
• Binding affinity: MOAD: Ki=22.3uM
  PDBbind-CN: -logKd/Ki=4.65,Ki=22.3uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H116 H118 D120 H196 C221 Y224 N233 H263
• Catalytic site (residue number reindexed from 1): H83 H85 D87 H148 C167 Y170 N179 H209
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process

External links

• PDB: RCSB:6dd1, PDBe:6dd1, PDBj:6dd1
• PDBsum: 6dd1
• PubMed: 31483651
• UniProt: Q9K2N0