Structure of PDB 6p55 Chain B Binding Site BS01

Receptor Information
>6p55 Chain B (length=327) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPG
RNRAVTDMIEPGSAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDT
HVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFP
GETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPL
SFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAK
TGTARKFVNGRYADNKHVATFIGFAPAKNPRVIVAVTIDEPTAHGYYGGV
VAGPPFKKIMGGSLNILGISPTKPLTA
Ligand information
Ligand IDNZM
InChIInChI=1S/C16H17N5O7S2/c1-2-7-5-29-14(20-11(7)15(26)27)8(3-22)18-13(25)12(21-28-4-10(23)24)9-6-30-16(17)19-9/h2-3,6,8,14,20H,1,4-5H2,(H2,17,19)(H,18,25)(H,23,24)(H,26,27)/b21-12-/t8-,14-/m1/s1
InChIKeyLIFBJXSMIMSLKH-VSOMHRBSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C=CC1=C(NC(SC1)C(C=O)NC(=O)C(=NOCC(=O)O)c2csc(n2)N)C(=O)O
OpenEye OEToolkits 2.0.7C=CC1=C(N[C@H](SC1)[C@@H](C=O)NC(=O)/C(=N\OCC(=O)O)/c2csc(n2)N)C(=O)O
CACTVS 3.385Nc1scc(n1)C(=NOCC(O)=O)C(=O)N[CH](C=O)[CH]2NC(=C(CS2)C=C)C(O)=O
CACTVS 3.385Nc1scc(n1)/C(=N/OCC(O)=O)C(=O)N[C@H](C=O)[C@@H]2NC(=C(CS2)C=C)C(O)=O
ACDLabs 12.01OC(=O)CO\N=C(/C(=O)NC(C=O)C1SCC(=C(N1)C(O)=O)[C@H]=C)c2csc(N)n2
FormulaC16 H17 N5 O7 S2
Namecefixime, bound form
ChEMBL
DrugBank
ZINC
PDB chain6p55 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6p55 Recognition of the beta-lactam carboxylate triggers acylation ofNeisseria gonorrhoeaepenicillin-binding protein 2.
Resolution1.74 Å
Binding residue
(original residue number in PDB)		S310 T347 S362 N364 F420 G421 Y422 T498 T500 A501 R502 H514
Binding residue
(residue number reindexed from 1)		S63 T100 S115 N117 F173 G174 Y175 T251 T253 A254 R255 H267
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:6p55, PDBe:6p55, PDBj:6p55
PDBsum6p55
PubMed31362987
UniProtP08149|PBP2_NEIGO Probable peptidoglycan D,D-transpeptidase PenA (Gene Name=penA)

[Back to BioLiP]