Structure of PDB 6xqv Chain B Binding Site BS02

Receptor Information
>6xqv 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]
DMLSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPGG
RNRAVTDMIEPGAAIKPFVIAKALDAGKTDLNERLNTQPYKIGPSPVRDT
HVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFP
GETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPL
SFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAK
TGTARKFVNGRYADNKHVATFIGFAPAKNPRVIVAVTIDEPTAHGYYGGV
VAGPPFKKIMGGSLNILGISPTKPLTA
Ligand information
Ligand ID9F2
InChIInChI=1S/C18H18N8O7S3/c1-25-18(22-12(28)13(29)23-25)36-4-6-3-34-15-9(14(30)26(15)10(6)16(31)32)21-11(27)8(24-33-2)7-5-35-17(19)20-7/h5,9,15H,3-4H2,1-2H3,(H2,19,20)(H,21,27)(H,23,29)(H,31,32)/b24-8+/t9-,15-/m1/s1
InChIKeyVAAUVRVFOQPIGI-TYHRLYECSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CON=C(C(=O)N[CH]1[CH]2SCC(=C(N2C1=O)C(O)=O)CSC3=NC(=O)C(=O)NN3C)c4csc(N)n4
OpenEye OEToolkits 2.0.6CN1C(=NC(=O)C(=O)N1)SCC2=C(N3C(C(C3=O)NC(=O)C(=NOC)c4csc(n4)N)SC2)C(=O)O
OpenEye OEToolkits 2.0.6CN1C(=NC(=O)C(=O)N1)SCC2=C(N3C([C@@H](C3=O)NC(=O)C(=NOC)c4csc(n4)N)SC2)C(=O)O
CACTVS 3.385CO/N=C(/C(=O)N[C@H]1[C@H]2SCC(=C(N2C1=O)C(O)=O)CSC3=NC(=O)C(=O)NN3C)c4csc(N)n4
FormulaC18 H18 N8 O7 S3
NameCeftriaxone
ChEMBLCHEMBL552182
DrugBank
ZINCZINC000008584434
PDB chain6xqv Chain B Residue 602 [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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PDB6xqv Mutations in PBP2 from ceftriaxone-resistant Neisseria gonorrhoeae alter the dynamics of the beta 3-beta 4 loop to favor a low-affinity drug-binding state.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		H348 V349 Y350 P351
Binding residue
(residue number reindexed from 1)		H101 V102 Y103 P104
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:6xqv, PDBe:6xqv, PDBj:6xqv
PDBsum6xqv
PubMed34529975
UniProtP08149|PBP2_NEIGO Probable peptidoglycan D,D-transpeptidase PenA (Gene Name=penA)

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