Structure of PDB 5vfd Chain A Binding Site BS01

Receptor Information

>5vfd Chain A (length=244) Species: 470 (Acinetobacter baumannii)

HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPAS
TFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVP
VYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVN
FADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGW
LTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII

Ligand information

• Ligand ID: 9CP
• InChI: InChI=1S/C8H13N3O6S/c1-5-2-7(8(9)13)11(4-12)3-6(5)10-17-18(14,15)16/h2,4,6-7,10H,3H2,1H3,(H2,9,13)(H,14,15,16)/t6-,7-/m0/s1
• InChIKey: XVMABMMPQCPJKI-BQBZGAKWSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC1=C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
  CACTVS 3.385: CC1=C[C@H](N(C[C@@H]1NO[S](O)(=O)=O)C=O)C(N)=O
  ACDLabs 12.01: C1(C=C(C)C(CN1C=O)NOS(O)(=O)=O)C(=O)N
  OpenEye OEToolkits 2.0.6: CC1=CC(N(CC1NOS(=O)(=O)O)C=O)C(=O)N
  CACTVS 3.385: CC1=C[CH](N(C[CH]1NO[S](O)(=O)=O)C=O)C(N)=O
• Formula: C8 H13 N3 O6 S
• Name: (2S,5R)-1-formyl-4-methyl-5-[(sulfooxy)amino]-1,2,5,6-tetrahydropyridine-2-carboxamide
• PDB chain: 5vfd Chain A Residue 306

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5vfd ETX2514 is a broad-spectrum beta-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii.
• Resolution: 1.93 Å
• Binding residue (original residue number in PDB): S81 Y112 W115 S128 V130 S219 G220 W221 R261
• Binding residue (residue number reindexed from 1): S50 Y81 W84 S97 V99 S188 G189 W190 R230
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S81 K84 S128 Y133 W167 W221
• Catalytic site (residue number reindexed from 1): S50 K53 S97 Y102 W136 W190

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding
• GO:0008800 beta-lactamase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0071555 cell wall organization

External links

• PDB: RCSB:5vfd, PDBe:5vfd, PDBj:5vfd
• PDBsum: 5vfd
• PubMed: 28665414
• UniProt: Q8RLA6