MolNFT v1 · #181081 · protein

Porcine dihydropyrimidine dehydrogenase (dpd) soaked with 5- ethynyluracil (5EU), NADPH - 20 minutes

7LJT · Dihydropyrimidine dehydrogenase [NADP(+)]: “Porcine dihydropyrimidine dehydrogenase (dpd) soaked with 5- ethynyluracil (5EU), NADPH - 20 minutes”. X-ray diffraction, 5 ligands (SF4, FAD, FMN), 20 pockets (best druggability 0.91).…

PDB: 7LJT
Type: protein
Length: 4,064 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropyrimidine dehydrogenase [NADP(+)]
EC: 1.3.1.2
UniProt: Q28943
Ligands: SF4, FAD, FMN, Y3G, NAP
Pockets: 20 · best druggability 0.91

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2)	protein	1016	36% helix, 17% strand	Q28943
B	Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2)	protein	1016	36% helix, 17% strand	Q28943
C	Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2)	protein	1015	36% helix, 16% strand	Q28943
D	Dihydropyrimidine dehydrogenase [NADP(+)] (EC 1.3.1.2)	protein	1017	36% helix, 17% strand	Q28943

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 16 copies · chains A, B, C, D
FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Y3G · 5-ethynylpyrimidine-2,4(1H,3H)-dione · ligand · 4 copies · chains A, B, C, D
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.91	0.94	185	FMN, Y3G
2	909	0.91	0.94	151	FMN, Y3G
3	1147	0.86	0.87	135	FAD, NAP
4	677	0.83	0.87	91	FAD, NAP
5	577	0.83	0.88	74	FAD, NAP

Interfaces

5 interfaces between chains.

A–B · 11997 Å² buried · 182 hydrogen bonds · protein-protein
C–D · 11861 Å² buried · 182 hydrogen bonds · protein-protein
A–D · 728 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 153 Å² buried · 1 hydrogen bond · protein-protein
B–D · 110 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7LJT · Porcine Dihydropyrimidine Dehydrogenase (DPD) soaked with 5-Ethynyluracil (5EU), NADPH… · the same entry in another collection · chain D against D, TM-score 1.00
Q28943 · AlphaFold monomer V2.0 prediction for dihydropyrimidine dehydrogenase [NADP(+)] (Q28943) · a predicted model of the same protein · chain C 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 Q28943
Elsewhere: RCSB PDB 7LJT · PDBe 7LJT · UniProt Q28943

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