Structure of PDB 6md8 Chain A Binding Site BS01

Receptor Information

>6md8 Chain A (length=263) Species: 562 (Escherichia coli)

PTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVM
AAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAA
ALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPG
DPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGL
PTSWTVGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRD
VLASAARIIAEGL

Ligand information

• Ligand ID: J84
• InChI: InChI=1S/C10H7Cl2N7/c11-5-1-2-8(7(12)3-5)19-9(13)6(4-14-19)10-15-17-18-16-10/h1-4H,13H2,(H,15,16,17,18)
• InChIKey: PZJPDMQBQCJCAX-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1cc(c(cc1Cl)Cl)n2c(c(cn2)c3[nH]nnn3)N
  CACTVS 3.385: Nc1n(ncc1c2[nH]nnn2)c3ccc(Cl)cc3Cl
  ACDLabs 12.01: c1(nnnn1)c3cnn(c2ccc(cc2Cl)Cl)c3N
• Formula: C10 H7 Cl2 N7
• Name: 1-(2,4-dichlorophenyl)-4-(1H-tetrazol-5-yl)-1H-pyrazol-5-amine
• ZINC: ZINC000000143018
• PDB chain: 6md8 Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6md8 Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): N104 Y105 S130 T235 G236 S237
• Binding residue (residue number reindexed from 1): N79 Y80 S105 T210 G211 S212
• Annotation score: 1
• Binding affinity: MOAD: Ki=4200uM
  PDBbind-CN: -logKd/Ki=2.38,Ki=4200uM

Enzymatic activity

• Catalytic site (original residue number in PDB): S70 K73 S130 E166 K234 S237
• Catalytic site (residue number reindexed from 1): S45 K48 S105 E141 K209 S212
• Enzyme Commision number: 3.5.2.6: beta-lactamase.

Gene Ontology

Molecular Function

• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0017001 antibiotic catabolic process
• GO:0030655 beta-lactam antibiotic catabolic process
• GO:0046677 response to antibiotic

External links

• PDB: RCSB:6md8, PDBe:6md8, PDBj:6md8
• PDBsum: 6md8
• PubMed: 30942078
• UniProt: Q9L5C7