MolNFT v1 · #156713 · protein
Crystal structure of human ppargamma ligand binding domain in complex with GW9662 and arachidonic acid
6MD2 · Peroxisome proliferator-activated receptor gamma: “Crystal structure of human ppargamma ligand binding domain in complex with GW9662 and arachidonic acid”. X-ray diffraction, 2 ligands (GW9, ACD), 9 pockets (best druggability 0.81).…
- PDB
- 6MD2
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- GW9, ACD
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 255 | 69% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 257 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- GW9 · 2-chloro-5-nitro-N-phenylbenzamide · ligand · 2 copies · chains A, B
- ACD · Arachidonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.81 | 0.83 | 73 | GW9, ACD |
| 2 | 523 | 0.80 | 0.86 | 50 | GW9, ACD |
| 3 | 138 | 0.59 | 0.84 | 20 | empty |
| 4 | 100 | 0.57 | 0.86 | 19 | empty |
| 5 | 225 | 0.51 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MD2 · Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and… · the same entry in another collection · chain A against A, TM-score 1.00
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 P37231
- Elsewhere: RCSB PDB 6MD2 · PDBe 6MD2 · UniProt P37231
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