Structure of PDB 8gbj Chain C Binding Site BS02

Receptor Information
>8gbj Chain C (length=317) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEAL
ETLQIIRREKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEI
CGAPGVGKTQLCMQLAVDVQIPECFGGVAGEAVFIDTEGSFMVDRVVDLA
TACIQHLQLIAEKHKGEEHRKALEDFTLDNILSHIYYFRCRDYTELLAQV
YLLPDFLSEHSKVRLVIVDGIAFPFRHDLDDLSLRTRLLNGLAQQMISLA
NNHRLAVILTNQMTTLVPALGESWGHAATIRLIFHWDRKQRLATLYKSPS
QKECTVLFQIKPQGFRD
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 C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8gbj Structural insights into BCDX2 complex function in homologous recombination.
Resolution3.11 Å
Binding residue
(original residue number in PDB)		P127 G128 G130 K131 T132 Q133 E161 R168 I341
Binding residue
(residue number reindexed from 1)		P104 G105 G107 K108 T109 Q110 E138 R145 I310
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:0008821 crossover junction DNA endonuclease activity
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0000707 meiotic DNA recombinase assembly
GO:0000722 telomere maintenance via recombination
GO:0000724 double-strand break repair via homologous recombination
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0007062 sister chromatid cohesion
GO:0007066 female meiosis sister chromatid cohesion
GO:0007131 reciprocal meiotic recombination
GO:0007141 male meiosis I
GO:0007283 spermatogenesis
GO:0010971 positive regulation of G2/M transition of mitotic cell cycle
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005657 replication fork
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0030054 cell junction
GO:0033063 Rad51B-Rad51C-Rad51D-XRCC2 complex
GO:0033065 Rad51C-XRCC3 complex
GO:0043231 intracellular membrane-bounded organelle
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8gbj, PDBe:8gbj, PDBj:8gbj
PDBsum8gbj
PubMed37344589
UniProtO43502|RA51C_HUMAN DNA repair protein RAD51 homolog 3 (Gene Name=RAD51C)

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