Structure of PDB 8gbj Chain X Binding Site BS02

Receptor Information
>8gbj Chain X (length=232) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSSLKEIEPNLFADGDILEFHGPEGTGKTEMLYHLTARCILPKSEGGLEV
EVLFIDTDYHFDMLRLVTILEHRLSQSSEEIIKYCLGRFFLVYCSSSTHL
LLTLYSLESMFCSHPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLRKC
SQCLEKLVNDYRLVLFATTQTIMQKAIDYRPYLCKAWQQLVKHRMFFSKQ
DSNQFSLVSRCLKSNSLKKHFFIIGESGVEFC
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain8gbj Chain X 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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PDB8gbj Structural insights into BCDX2 complex function in homologous recombination.
Resolution3.11 Å
Binding residue
(original residue number in PDB)		E50 G51 T52 G53 K54 T55 E56 R91 I272 G273 E274
Binding residue
(residue number reindexed from 1)		E24 G25 T26 G27 K28 T29 E30 R65 I224 G225 E226
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000400 four-way junction DNA binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0000278 mitotic cell cycle
GO:0000724 double-strand break repair via homologous recombination
GO:0001701 in utero embryonic development
GO:0001756 somitogenesis
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006974 DNA damage response
GO:0007098 centrosome cycle
GO:0010165 response to X-ray
GO:0010332 response to gamma radiation
GO:0022008 neurogenesis
GO:0035264 multicellular organism growth
GO:0042148 DNA strand invasion
GO:0043524 negative regulation of neuron apoptotic process
GO:0050769 positive regulation of neurogenesis
GO:0051321 meiotic cell cycle
GO:2000269 regulation of fibroblast apoptotic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005657 replication fork
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005856 cytoskeleton
GO:0033063 Rad51B-Rad51C-Rad51D-XRCC2 complex
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8gbj, PDBe:8gbj, PDBj:8gbj
PDBsum8gbj
PubMed37344589
UniProtO43543|XRCC2_HUMAN DNA repair protein XRCC2 (Gene Name=XRCC2)

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