Structure of PDB 2pmk Chain A Binding Site BS01

Receptor Information
>2pmk Chain A (length=243) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHDITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKL
IQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNIS
LANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRI
AIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRL
STVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD
Ligand information
Ligand ID128
InChIInChI=1S/C16H17N8O19P3/c17-13-10-14(19-4-18-13)21(5-20-10)15-12-11(7(39-15)3-38-45(34,35)43-46(36,37)42-44(31,32)33)40-16(41-12)8(23(27)28)1-6(22(25)26)2-9(16)24(29)30/h1-2,4-5,7,11-12,15H,3H2,(H,25,26)(H,34,35)(H,36,37)(H2,17,18,19)(H2,31,32,33)/t7-,11-,12-,15-/m1/s1
InChIKeyXFMMHXLUHKBKQE-UHEGPQQHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH]4O[C]5(O[CH]34)C(=C[C](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N
CACTVS 3.385Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@H]4O[C]5(O[C@@H]34)C(=C[C@@](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O
ACDLabs 12.01P(=O)(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(C2C1OC3(O2)C(=C/C(C=C3[N+](=O)[O-])=[N+](/O)[O-])[N+](=O)[O-])n4cnc5c(N)ncnc45
FormulaC16 H17 N8 O19 P3
NameSPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE
ChEMBL
DrugBankDB02524
ZINCZINC000096900390
PDB chain2pmk Chain A Residue 301 [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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PDB2pmk Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex
Resolution1.6 Å
Binding residue
(original residue number in PDB)		Y477 G505 S506 G507 K508 S509 T510 K513
Binding residue
(residue number reindexed from 1)		Y13 G41 S42 G43 K44 S45 T46 K49
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=5.92,Kd=1.2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity

View graph for
Molecular Function
External links
PDB RCSB:2pmk, PDBe:2pmk, PDBj:2pmk
PDBsum2pmk
PubMed18155559
UniProtP08716|HLYBP_ECOLX Alpha-hemolysin translocation ATP-binding protein HlyB (Gene Name=hlyB)

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