MolNFT v1 · #134143 · protein
IDH1 R132H in complex with IDH125
5SVF · Isocitrate dehydrogenase [NADP] cytoplasmic: “IDH1 R132H in complex with IDH125”. X-ray diffraction, 2 ligands (NDP, 70P), 19 pockets (best druggability 0.86). MolNFT v1 #134143 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5SVF
- Type
- protein
- Length
- 1,596 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
- NDP, 70P
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 398 | 47% helix, 23% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 399 | 46% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 397 | 47% helix, 23% strand | O75874 |
| D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 402 | 47% helix, 23% strand | O75874 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- 70P · (4S)-3-(2-{[(1S)-1-phenylethyl]amino}pyrimidin-4-yl)-4-(propan-2-yl)-1,3-oxazolidin-2-one · ligand · 4 copies · chains A, C, B, D
- FLC · Citrate anion · additive · 4 copies · chains A, C, B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.86 | 0.87 | 101 | 70P |
| 2 | 1031 | 0.85 | 0.86 | 89 | 70P |
| 3 | 465 | 0.66 | 0.78 | 54 | NDP |
| 4 | 370 | 0.65 | 0.79 | 43 | empty |
| 5 | 418 | 0.64 | 0.78 | 56 | NDP |
Interfaces
3 interfaces between chains.
- B–D · 2736 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 2680 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 721 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · 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 O75874
- Elsewhere: RCSB PDB 5SVF · PDBe 5SVF · UniProt O75874
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