MolNFT v1 · #97368 · protein

Human dihydrofolate reductase complexed with NADPH and 5-{3-[3-(3,5- pyrimidine)]-phenyl-prop-1-yn-1-yl}-6-ethyl-pyrimidine-2,4DIAMINE

4KBN: “Human dihydrofolate reductase complexed with NADPH and 5-{3-[3-(3,5…”. X-ray diffraction, 6 ligands (25U, NDP, MG), 4 pockets (best druggability 0.72). MolNFT v1 #97368 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4KBN
Type: protein
Length: 372 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrofolate reductase
EC: 1.5.1.3
UniProt: P00374
Ligands: 25U, NDP, MG, SR, CL, NH4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dihydrofolate reductase (EC 1.5.1.3)	protein	186	20% helix, 34% strand	P00374

Ligands and binding sites

25U · 6-ethyl-5-{3-[3-(pyrimidin-5-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 9 copies · chains A, B
SR · Strontium ion · metal · chains A, B
CL · Chloride ion · ion · 8 copies · chains A, B
NH4 · Ammonium ion · ion · chains B
EOH · Ethanol · additive · 3 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	602	0.72	0.80	62	25U, CL, NDP
2	489	0.72	0.81	49	25U, NDP
3	206	0.66	0.85	31	CL, MG
4	55	0.29	0.75	21	empty

Interfaces

1 interface between chains.

A–B · 438 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4KBN · human dihydrofolate reductase complexed with NADPH and… · the same entry in another collection · chain A against A, TM-score 1.00
P00374 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P00374) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P00374
Elsewhere: RCSB PDB 4KBN · PDBe 4KBN · UniProt P00374

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