MolNFT v1 · #145377 · protein

SAMHD1 hd domain bound to decitabine triphosphate

6CM2 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “SAMHD1 hd domain bound to decitabine triphosphate”. X-ray diffraction, 3 ligands (F6G, GTP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #145377 on GenesisL1: 3D…

PDB: 6CM2
Type: protein
Length: 1,923 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: F6G, GTP, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, B	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	481	52% helix, 12% strand	Q9Y3Z3
A	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-)	protein	480	53% helix, 12% strand	Q9Y3Z3

Ligands and binding sites

F6G · 6-amino-3-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,4-dihydro-1,3,5-triazin-2(1H)-one · ligand · 8 copies · chains D, C, B, A
GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, B, A, C
MG · Magnesium ion · metal · 4 copies · chains D, C, B, A

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	655	0.85	0.89	83	GTP, F6G, MG
2	642	0.85	0.89	79	GTP, F6G, MG
3	481	0.84	0.91	77	F6G, GTP
4	411	0.84	0.92	67	F6G
5	145	0.82	0.98	29	empty

Interfaces

6 interfaces between chains.

C–A · 2198 Å² buried · 30 hydrogen bonds · protein-protein
D–B · 2172 Å² buried · 32 hydrogen bonds · protein-protein
C–B · 1922 Å² buried · 21 hydrogen bonds · protein-protein
D–A · 1899 Å² buried · 21 hydrogen bonds · protein-protein
B–A · 494 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6CM2 · SAMHD1 HD domain bound to decitabine triphosphate · the same entry in another collection · chain D against D, 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 6CM2 · PDBe 6CM2 · UniProt Q9Y3Z3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.