MolNFT v1 · #4257 · protein
Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with NADP and inhibitor LY374571
1DIG: “Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with NADP and inhibitor LY374571”. X-ray diffraction, 2 ligands (NAP, L37), 5 pockets (best druggability 0.67). MolNFT v1 #4257 on GenesisL1: 3D structure…
- PDB
- 1DIG
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylenetetrahydrofolate dehydrogenase / cyclohydrolase
- EC
- 1.5.1.5, 3.5.4.9
- UniProt
- P11586
- Ligands
- NAP, L37
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylenetetrahydrofolate dehydrogenase / cyclohydrolase (EC 1.5.1.5, 3.5.4.9) | protein | 285 | 41% helix, 16% strand | P11586 |
| B | Methylenetetrahydrofolate dehydrogenase / cyclohydrolase (EC 1.5.1.5, 3.5.4.9) | protein | 295 | 40% helix, 17% strand | P11586 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- L37 · [[N'-(2,5-diamino-6-hydroxy-pyrimidin-4-yl)-ureayl]-phen-4-yl]-carbonyl-glutamic acid · ligand · chains A
- ACT · Acetate ion · additive · chains 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 | 487 | 0.67 | 0.78 | 49 | NAP, L37 |
| 2 | 294 | 0.57 | 0.76 | 31 | empty |
| 3 | 54 | 0.49 | 0.86 | 18 | empty |
| 4 | 72 | 0.46 | 0.82 | 17 | empty |
| 5 | 65 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1405 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 1DIG · Human methylenetetrahydrofolate dehydrogenase / cyclohydrolase complexed with NADP and… · the same entry in another collection · chain A against A, TM-score 1.00
- P11586 · AlphaFold monomer V2.0 prediction for C-1-tetrahydrofolate synthase, cytoplasmic (P11586) · a predicted model of the same protein · chain A 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 P11586
- Elsewhere: RCSB PDB 1DIG · PDBe 1DIG · UniProt P11586
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