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Crystal structure of human IDH1 mutant (R132H) in complex with NADP+ and an inhibitor related to bay 1436032
Analyse Crystal structure of human IDH1 mutant (R132H) in complex with NADP+ and an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LGE
- Type
- protein
- Length
- 1,639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- NAP, 6VN
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 406 | 46% helix, 21% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 407 | 46% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 414 | 45% helix, 21% strand | O75874 |
| D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 45% helix, 22% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 6VN · 2-[(4-propan-2-ylphenyl)amino]-1-[(1~{S},5~{S})-3,3,5-trimethylcyclohexyl]benzimidazole-5-carboxylic acid · ligand · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.84 | 0.94 | 37 | 6VN |
| 2 | 280 | 0.84 | 0.94 | 38 | 6VN |
| 3 | 1083 | 0.75 | 0.78 | 94 | NAP |
| 4 | 1094 | 0.74 | 0.77 | 90 | NAP |
| 5 | 743 | 0.73 | 0.79 | 60 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3137 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2995 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 346 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 135 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LGE · Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor… · the same entry in another collection · chain B against B, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain D 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 O75874
- Elsewhere: RCSB PDB 5LGE · PDBe 5LGE · UniProt O75874
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