Structure of PDB 6mdw Chain A Binding Site BS01

Receptor Information
>6mdw Chain A (length=185) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSLVDASWELVDPTPDLQALFVQFNDQFFWGQLEAVEVKWSVRMTLCAG
ICSYEGGMCSIRLSEPLLKLRPRKDLVETLLHEMIHAYLFVTNNDKDREG
HGPEFCKHMHRINSLTGANITVYHTFHDEVDEYRRHWWRCNGPCQHRPPY
YGYVKRATNREPSAHDYWWAEHQKTCGGTYIKIKE
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6mdw Chain A Residue 802 [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]
PDB6mdw Structural Insight into DNA-Dependent Activation of Human Metalloprotease Spartan.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		L74 Y179 Y182 V183 R189 Y196 W197 Y209
Binding residue
(residue number reindexed from 1)		L47 Y150 Y153 V154 R160 Y167 W168 Y180
Annotation score4
Enzymatic activity
Enzyme Commision number 3.4.24.-
Gene Ontology
Molecular Function
GO:0003697 single-stranded DNA binding
GO:0004222 metalloendopeptidase activity
Biological Process
GO:0006974 DNA damage response

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6mdw, PDBe:6mdw, PDBj:6mdw
PDBsum6mdw
PubMed30893605
UniProtQ9H040|SPRTN_HUMAN DNA-dependent metalloprotease SPRTN (Gene Name=SPRTN)

[Back to BioLiP]