MolNFT v2 · #116954 · protein
Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl prope inhibitor 17
5DKH · Probable global transcription activator SNF2L2: “Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl prope inhibitor 17”. X-ray diffraction at 1.7, 2 ligands (5C0, ZN), 3 pockets (best…
- PDB
- 5DKH
- Type
- protein
- Length
- 339 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Homo sapiens
- Molecule
- Probable global transcription activator SNF2L2
- EC
- 3.6.4.-
- UniProt
- P51531
- Ligands
- 5C0, ZN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · resolution 1.7 · 3 distinct chains · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable global transcription activator SNF2L2 (EC 3.6.4.-) | protein | 116 | 63% helix, 2% strand | P51531 |
| B | Probable global transcription activator SNF2L2 (EC 3.6.4.-) | protein | 110 | 65% helix, 2% strand | P51531 |
| C | Probable global transcription activator SNF2L2 (EC 3.6.4.-) | protein | 113 | 65% helix, 2% strand | P51531 |
Ligands and binding sites
- 5C0 · (2E)-3-[(6S,9R)-4-(cyclopropylamino)-6,7,8,9-tetrahydro-5H-6,9-epiminocyclohepta[d]pyrimidin-10-yl]-1-(2-hydroxyphenyl)prop-2-en-1-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.71 | 0.76 | 76 | 5C0 |
| 2 | 72 | 0.48 | 0.83 | 16 | empty |
| 3 | 51 | 0.43 | 0.83 | 16 | 5C0 |
Interfaces
3 interfaces between chains.
- B–C · 203 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DKH · Crystal structure of the bromodomain of human brm (SMARCA2) in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P51531 · AlphaFold monomer V2.0 prediction for probable global transcription activator SNF2L2… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P51531
- Elsewhere: RCSB PDB 5DKH · PDBe 5DKH · UniProt P51531
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