Structure of PDB 6xu1 Chain B Binding Site BS04

Receptor Information

>6xu1 Chain B (length=479) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DTMKVINDPIHGHIELHPLLVRIIDTPQFQRLRYIKQLGGGYYVFPGASH
NRFEHSLGVGYLAGCLVHALGEKQPELQISERDVLCVQIAGLCHDLGHGP
FSAMFDGRFIPLARPEVKWTHEQGSVMMFEHLINSNGIKPVMEQYGLIPE
EDICFIKEQIVGPLLWPYKGRPENKSFLYEIVSNKRNGIDVDKWDYFARD
CHHLGIQNNFDYKRFIKFARVCEVDNELRICARDKEVGNLYDMFHTRNSL
HRRAYQHKVGNIIDTMITDAFLKADDYIEITGAGGKKYRISTAIDDMEAY
TKLTDNIFLEILYSTDPKLKDAREILKQIEYRNLFKYVGETQPTGQIKIK
REDYESLPKEVASAKPKVLLDVKLKAEDFIVDVINMDYGMQEKNPIDHVS
FYCKTAPNRAIRITKNQVSQLLPEKFAEQLIRVYCKKVDRKSLYAARQYF
VQWCADRNFTKPQDGDVIAPLITPQKKEW

Ligand information

Ligand ID

DZ4

InChI

InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1

InChIKey

WKIPJDSLGCBQCU-RRKCRQDMSA-N

SMILES

Software	SMILES
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0	c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0	c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H17 N6 O11 P3

Name

2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine

PDB chain

6xu1 Chain B Residue 705 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6xu1 Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis.
Resolution	2.2 Å
Binding residue (original residue number in PDB)	Q149 L150 R164 D207 A215 H233 D311 K312 Y315 D319 R366 Y374
Binding residue (residue number reindexed from 1)	Q37 L38 R52 D95 A103 H121 D192 K193 Y196 D200 R247 Y255
Annotation score	1
Binding affinity	MOAD: Ki=0.78uM

Enzymatic activity

Enzyme Commision number

3.1.5.-

External links

PDB	RCSB:6xu1, PDBe:6xu1, PDBj:6xu1
PDBsum	6xu1
PubMed	32576829
UniProt	Q9Y3Z3\|SAMH1_HUMAN Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (Gene Name=SAMHD1)

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