MolNFT v1 · #117519 · protein

Crystal structure of NAD(P)H dehydrogenase, quinone 1 complexed with a chemotherapeutic naphthoquinone E6A

5EAI · NAD(P)H dehydrogenase [quinone] 1: “Crystal structure of NAD(P)H dehydrogenase, quinone 1 complexed with a chemotherapeutic naphthoquinone E6A”. X-ray diffraction, 2 ligands (FAD, E6A), 20 pockets (best druggability 0.87). MolNFT v1…

PDB: 5EAI
Type: protein
Length: 3,799 residues
Chains: 14
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD(P)H dehydrogenase [quinone] 1
EC: 1.6.5.2
UniProt: P15559
Ligands: FAD, E6A
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	270	40% helix, 16% strand	P15559
C, G, I	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	272	39% helix, 16% strand	P15559
D	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	271	38% helix, 15% strand	P15559
E, F, H, J, K, N	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	271	35% helix, 16% strand	P15559
L, M	NAD(P)H dehydrogenase [quinone] 1 (EC 1.6.5.2)	protein	273	39% helix, 15% strand	P15559

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 14 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
E6A · (2~{R},3~{R})-2-[(2~{S},3~{S})-3-bromanyl-1,4-bis(oxidanylidene)-2,3-dihydronaphthalen-2-yl]-3-oxidanyl-2,3-dihydronaphthalene-1,4-dione · ligand · 5 copies · chains A, B, E, F, K, G, H, I, L, M, N

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	949	0.87	0.88	103	empty
2	988	0.86	0.87	103	empty
3	705	0.84	0.88	63	FAD
4	654	0.83	0.88	58	FAD, E6A
5	780	0.83	0.86	68	E6A, FAD

Interfaces

26 interfaces between chains.

K–L · 2823 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 2813 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 2796 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 2794 Å² buried · 30 hydrogen bonds · protein-protein
M–N · 2787 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

5EAI · Crystal Structure of NAD(P)H dehydrogenase, qui 1 complexed with a chemotherapeutic… · the same entry in another collection · chain N against N, 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 P15559
Elsewhere: RCSB PDB 5EAI · PDBe 5EAI · UniProt P15559

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