Structure of PDB 6yom Chain A Binding Site BS04

Receptor Information
>6yom Chain A (length=470) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TMKVINDPIHGHIELHPLLVRIINTPQFQRLRYIKQLGGGYYVFPGASHN
RFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGPF
SHMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPEE
DICFIKEQIVGPLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARDCH
HLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSLHR
RAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAYTK
LTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIKRE
DYESLPKEVASAKPKKAEDFIVDVINMDYGMQEKNPIDHVSFYCKTAPNR
AIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYFVQWCADRNF
TKPQDGDVIAPLITPQKKEW
Ligand information
Ligand IDCZF
InChIInChI=1S/C10H15N4O15P3/c15-5-3(1-26-31(22,23)29-32(24,25)28-30(19,20)21)27-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1
InChIKeyCAEFEWVYEZABLA-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23
OpenEye OEToolkits 2.0.7c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)NC(=O)NC2=O
CACTVS 3.385O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23
OpenEye OEToolkits 2.0.7c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)NC(=O)NC2=O
FormulaC10 H15 N4 O15 P3
Name[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate;
xanthosine triphosphate
ChEMBLCHEMBL4443439
DrugBank
ZINC
PDB chain6yom Chain A Residue 706 [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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PDB6yom Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.
Resolution3.25 Å
Binding residue
(original residue number in PDB)
K116 V117 I118 N137 R145
Binding residue
(residue number reindexed from 1)
K3 V4 I5 N24 R32
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.5.-
External links
PDB RCSB:6yom, PDBe:6yom, PDBj:6yom
PDBsum6yom
PubMed32576829
UniProtQ9Y3Z3|SAMH1_HUMAN Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (Gene Name=SAMHD1)

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