Structure of PDB 6vbd Chain A Binding Site BS01

Receptor Information

>6vbd Chain A (length=324) Species: 485 (Neisseria gonorrhoeae)

ALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALVNTPGRN
RAVTDMIEPGSVMKPFPIAKALDSGKVDTTDTFNTLPYKIGPATVQDTHV
YPTLDVRGIMQKSSNVGTSKLSAMFTPKEMYDFYHDLGVGVRMHSGFPGE
SAGVLRNWRKWRPIEQATMSFGYGLQLSLLQLARAYTVLTHDGELLPVSF
EKQAVAPKGKRVIKASTAKKVRELMVSVTEAGGSGIAGAVDGFDVGAKTG
TARKLVNGRYVDYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVT
GPVFKQVMGGSLNILGVSPTKPLT

Ligand information

• Ligand ID: CEF
• InChI: InChI=1S/C14H15N5O5S2/c1-6-4-25-12(18-9(6)13(22)23)7(3-20)16-11(21)10(19-24-2)8-5-26-14(15)17-8/h3,5,7,12H,1,4H2,2H3,(H2,15,17)(H,16,21)(H,22,23)/b19-10-/t7-,12-/m1/s1
• InChIKey: NRYMPLKBKFIWQC-YVCCLBOHSA-N
• SMILES:
  CACTVS 3.385: CO\N=C(/C(=O)N[C@H](C=O)[C@H]1SCC(=C)C(=N1)C(O)=O)c2csc(N)n2
  OpenEye OEToolkits 1.7.6: CO/N=C(/c1csc(n1)N)\C(=O)NC(C=O)C2N=C(C(=C)CS2)C(=O)O
  OpenEye OEToolkits 1.7.6: CON=C(c1csc(n1)N)C(=O)NC(C=O)C2N=C(C(=C)CS2)C(=O)O
  CACTVS 3.385: CON=C(C(=O)N[CH](C=O)[CH]1SCC(=C)C(=N1)C(O)=O)c2csc(N)n2
• Formula: C14 H15 N5 O5 S2
• Name: CEFOTAXIME, C3' cleaved, open, bound form
• DrugBank: DB08375
• ZINC: ZINC000015605562
• PDB chain: 6vbd Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vbd Mutations in Neisseria gonorrhoeae penicillin-binding protein 2 associated with extended-spectrum cephalosporin resistance create an energetic barrier against acylation via restriction of protein dynamics
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): S310 K313 T347 N364 G499 T500 Y544 S545
• Binding residue (residue number reindexed from 1): S61 K64 T98 N115 G250 T251 Y295 S296
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.

Gene Ontology

Molecular Function

• GO:0008658 penicillin binding

External links

• PDB: RCSB:6vbd, PDBe:6vbd, PDBj:6vbd
• PDBsum: 6vbd
• UniProt: F2Z7K9