Structure of PDB 7c98 Chain B Binding Site BS04

Receptor Information
>7c98 Chain B (length=309) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDIDLLQKHGINVADIKKLKSVGICTIKGIQMTTRRALCNVKGLSEAKVD
KIKEAANKLIEPGFLTAFEYSEKRKMVFHITTGSQEFDKLLGGGIESMAI
TEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLR
DIADRFNVDHDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLI
IDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMT
ADPGAPKKPIGGHILAHASTTRISLRKGRGELRIAKIYDSPEMPENEATF
AITAGGIGD
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 chain7c98 Chain B Residue 402 [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]
PDB7c98 Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures.
Resolution3.47 Å
Binding residue
(original residue number in PDB)		F128 G131 K132 T133 Q134 R169 I330 T331 A332
Binding residue
(residue number reindexed from 1)		F107 G110 K111 T112 Q113 R148 I302 T303 A304
Annotation score3
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000150 DNA strand exchange activity
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0016887 ATP hydrolysis activity
GO:0042802 identical protein binding
GO:0140664 ATP-dependent DNA damage sensor activity
Biological Process
GO:0000724 double-strand break repair via homologous recombination
GO:0000730 DNA recombinase assembly
GO:0001541 ovarian follicle development
GO:0001556 oocyte maturation
GO:0006259 DNA metabolic process
GO:0006281 DNA repair
GO:0006312 mitotic recombination
GO:0007129 homologous chromosome pairing at meiosis
GO:0007131 reciprocal meiotic recombination
GO:0007141 male meiosis I
GO:0007276 gamete generation
GO:0007283 spermatogenesis
GO:0007286 spermatid development
GO:0007292 female gamete generation
GO:0042148 DNA strand invasion
GO:0048477 oogenesis
GO:0051321 meiotic cell cycle
GO:0070192 chromosome organization involved in meiotic cell cycle
GO:1990918 double-strand break repair involved in meiotic recombination
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0000794 condensed nuclear chromosome
GO:0000800 lateral element
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0035861 site of double-strand break

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7c98, PDBe:7c98, PDBj:7c98
PDBsum7c98
PubMed33446654
UniProtQ14565|DMC1_HUMAN Meiotic recombination protein DMC1/LIM15 homolog (Gene Name=DMC1)

[Back to BioLiP]