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5'-diphenyl nucleoside inhibitors of plasmodium falciparum dutpase

Analyse 5'-diphenyl nucleoside inhibitors of plasmodium falciparum dutpase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3T70
Type: protein
Length: 437 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative; Peptide gly-his-gly
EC: 3.6.1.23
UniProt: Q8II92
Ligands: DU4, SO4
Pockets: 5 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative (EC 3.6.1.23)	protein	149	9% helix, 42% strand	Q8II92
B	Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative (EC 3.6.1.23)	protein	137	9% helix, 45% strand	Q8II92
C	Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative (EC 3.6.1.23)	protein	148	9% helix, 40% strand	Q8II92
F	Peptide gly-his-gly	protein	3	0% helix, 0% strand	—

Ligands and binding sites

DU4 · 2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine · ligand · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 6 copies · chains A, C, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.71	0.84	34	empty
2	608	0.69	0.78	62	empty
3	180	0.52	0.78	24	SO4, DU4
4	184	0.51	0.77	25	DU4, SO4
5	143	0.47	0.77	25	DU4, SO4

Interfaces

5 interfaces between chains.

A–C · 1000 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 985 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 984 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 169 Å² buried · 3 hydrogen bonds · protein-protein
B–F · 130 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3T70 · 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase · the same entry in another collection · chain A against A, 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 Q8II92
Elsewhere: RCSB PDB 3T70 · PDBe 3T70 · UniProt Q8II92

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