Research workbench
Crystal structure of dihydrofolate reductase from mycobacterium tuberculosis bound to NADP and sddc inhibitor sddc-23
Analyse Crystal structure of dihydrofolate reductase from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SCP
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrofolate reductase
- EC
- 1.5.1.3
- UniProt
- P9WNX1
- Ligands
- NAP, GWL, CL
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrofolate reductase (EC 1.5.1.3) | protein | 168 | 18% helix, 32% strand | P9WNX1 |
| B | Dihydrofolate reductase (EC 1.5.1.3) | protein | 166 | 19% helix, 32% strand | P9WNX1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GWL · 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl) oxy]propoxy}phenyl)propanamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.72 | 0.81 | 46 | NAP, EDO, GWL |
| 2 | 495 | 0.72 | 0.81 | 44 | NAP, EDO, GWL |
| 3 | 474 | 0.68 | 0.80 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5SCP · Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to… · the same entry in another collection · chain A against A, 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 0.95
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 5SCP · PDBe 5SCP · UniProt P9WNX1
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