Structure of PDB 8vep Chain A Binding Site BS01

Receptor Information
>8vep Chain A (length=324) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALVNTPGRN
RAVTDMIEPGSVMKPFPIAKALDSGKVDTTDTFNTLPYKIGPATVQDTHV
YPTLDVRGIMQKSSNVGTSKLSAMFTPKEMYDFYHDLGVGVRMHSGFPGE
SAGVLRNWRKWRPIEQATMSFGYGLQLSLLQLARAYTVLTHDGELLPVSF
EKQAVAPKGKRVIKASTAKKVRELMVSVTEAGGSGIAGAVDGFDVGAKTG
TARKLVNGRYVDYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVT
GPVFKQVMGGSLNILGVSPTKPLT
Ligand information
Ligand IDJPP
InChIInChI=1S/C23H29N5O7S/c1-4-27-10-11-28(20(32)19(27)31)22(35)25-15(13-8-6-5-7-9-13)17(30)24-14(12-29)18-26-16(21(33)34)23(2,3)36-18/h5-9,12,14-16,18,26H,4,10-11H2,1-3H3,(H,24,30)(H,25,35)(H,33,34)/t14-,15-,16+,18-/m1/s1
InChIKeyCJYMHKMECTVNSA-XLMAVXFVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C@H](C=O)[C@@H]3N[C@H](C(S3)(C)C)C(=O)O
CACTVS 3.385CCN1CCN(C(=O)N[C@@H](C(=O)N[C@H](C=O)[C@@H]2N[C@@H](C(O)=O)C(C)(C)S2)c3ccccc3)C(=O)C1=O
OpenEye OEToolkits 1.7.6CCN1CCN(C(=O)C1=O)C(=O)NC(c2ccccc2)C(=O)NC(C=O)C3NC(C(S3)(C)C)C(=O)O
ACDLabs 12.01O=C(NC(C=O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)NC(=O)N3C(=O)C(=O)N(CC)CC3
CACTVS 3.385CCN1CCN(C(=O)N[CH](C(=O)N[CH](C=O)[CH]2N[CH](C(O)=O)C(C)(C)S2)c3ccccc3)C(=O)C1=O
FormulaC23 H29 N5 O7 S
NamePiperacillin (Open Form)
ChEMBL
DrugBank
ZINCZINC000098209054
PDB chain8vep Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8vep Ureidopenicillins Are Potent Inhibitors of Penicillin-Binding Protein 2 from Multidrug-Resistant Neisseria gonorrhoeae H041.
Resolution2.002 Å
Binding residue
(original residue number in PDB)		S310 T347 S362 N364 Y422 T498 G499 T500 R502 Y509 Y544
Binding residue
(residue number reindexed from 1)		S61 T98 S113 N115 Y173 T249 G250 T251 R253 Y260 Y295
Annotation score1
Enzymatic activity
Enzyme Commision number 3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase.
Gene Ontology
Molecular Function
GO:0008658 penicillin binding

View graph for
Molecular Function
External links
PDB RCSB:8vep, PDBe:8vep, PDBj:8vep
PDBsum8vep
PubMed38446051
UniProtF2Z7K9

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