MolNFT v1 · #62406 · protein
Candida glabrata dihydrofolate reductase complexed with 2,4-diamino-5- [3-methyl-3-(3-methoxy-5-PHENYLPHENYL)PROP-1-ynyl]-6- METHYLPYRIMIDINE(UCP111D) and NADPH
3EEJ: “Candida glabrata dihydrofolate reductase complexed with 2,4-diamino-5…”. X-ray diffraction, 2 ligands (NDP, 53R), 5 pockets (best druggability 0.83). MolNFT v1 #62406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3EEJ
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- UniProt
- Q6FPH0
- Ligands
- NDP, 53R
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrofolate reductase | protein | 225 | 24% helix, 35% strand | Q6FPH0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 53R · 5-[(3R)-3-(5-methoxybiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine · ligand · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.83 | 0.83 | 102 | NDP, 53R |
| 2 | 571 | 0.64 | 0.76 | 55 | empty |
| 3 | 53 | 0.43 | 0.82 | 14 | empty |
| 4 | 53 | 0.41 | 0.82 | 13 | empty |
| 5 | 50 | 0.28 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1226 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3EEJ · Candida glabrata Dihydrofolate Reductase complexed with… · 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 Q6FPH0
- Elsewhere: RCSB PDB 3EEJ · PDBe 3EEJ · UniProt Q6FPH0
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