MolNFT v1 · #187143 · protein

SAMHD1 hd domain bound to cndac

7S2Y · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “SAMHD1 hd domain bound to cndac”. X-ray diffraction, 4 ligands (85T, DTP, GTP), 20 pockets (best druggability 0.89). MolNFT v1 #187143 on GenesisL1: 3D structure, binding…

PDB: 7S2Y
Type: protein
Length: 1,924 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
EC: 3.1.5.-
UniProt: Q9Y3Z3
Ligands: 85T, DTP, GTP, MG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	481	52% helix, 13% strand	Q9Y3Z3

Ligands and binding sites

85T · 4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains B, C, D, A
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	921	0.89	0.92	133	DTP, GTP
2	881	0.89	0.92	135	DTP, GTP
3	158	0.83	0.98	27	empty
4	144	0.82	0.99	26	empty
5	955	0.76	0.79	77	85T, MG

Interfaces

6 interfaces between chains.

A–C · 2211 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 2184 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 1925 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1925 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 510 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7S2Y · SAMHD1 HD domain bound to CNDAC · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y3Z3
Elsewhere: RCSB PDB 7S2Y · PDBe 7S2Y · UniProt Q9Y3Z3

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