MolNFT v1 · #146309 · protein
Mycobacterium tuberculosis dihydrofolate reductase complexed with beta-NADPH and 3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-YL)BUT-3- yn-2-yl]-5'-METHOXY[1,1'-biphenyl]-4-carboxylic acid
6DDP: “Mycobacterium tuberculosis dihydrofolate reductase complexed with beta-NADPH and…”. X-ray diffraction, 2 ligands (NDP, G6Y), 9 pockets (best druggability 0.74). MolNFT v1 #146309 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6DDP
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P9WNX1
- Ligands
- NDP, G6Y
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydrofolate reductase (EC 1.5.1.3) | protein | 159 | 21% helix, 35% strand | P9WNX1 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- G6Y · 3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.74 | 0.80 | 74 | NDP, G6Y |
| 2 | 540 | 0.73 | 0.81 | 50 | NDP, G6Y |
| 3 | 513 | 0.72 | 0.81 | 48 | NDP, G6Y |
| 4 | 502 | 0.71 | 0.80 | 46 | G6Y, NDP |
| 5 | 170 | 0.43 | 0.74 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–D · 559 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 547 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 542 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6DDP · Mycobacterium tuberculosis Dihydrofolate Reductase complexed with beta-NADPH and… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WNX1 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P9WNX1) · a predicted model of the same protein · chain B 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 P9WNX1
- Elsewhere: RCSB PDB 6DDP · PDBe 6DDP · UniProt P9WNX1
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