MolNFT v1 · #32857 · protein

Human dihydrofolate reductase complexed with NADPH and 2,4-diamino-5- ((7,8-dicarbaundecaboran-7-YL)METHYL)-6-methylpyrimidine, a novel boron containing, nonclassical antifolate

2C2T: “Human dihydrofolate reductase complexed with NADPH and 2,4-diamino-5…”. X-ray diffraction, 3 ligands (NDP, 39B, 39E), 3 pockets (best druggability 0.77). MolNFT v1 #32857 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2C2T
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: NDP, 39B, 39E
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dihydrofolate reductase (EC 1.5.1.3)	protein	186	20% helix, 33% strand	P00374

Ligands and binding sites

NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
39B · (S)-2,4-diamino-5-((7,8-dicarbaundecaboran-7-yl) methyl)-6-methylpyrimidine · ligand · 2 copies · chains A, B
39E · (R)-2,4-diamino-5-((7,8-dicarbaundecaboran-7-yl) methyl)-6-methylpyrimidine · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.77	0.79	76	NDP, 39B, 39E
2	543	0.73	0.81	49	NDP, 39B, 39E
3	67	0.38	0.79	13	empty

Interfaces

1 interface between chains.

A–B · 333 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2C2T · 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 A against A, TM-score 0.99

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 2C2T · PDBe 2C2T · UniProt P00374

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