Research workbench
TAF1-BD2 in complex with CPD27 (6-(but-3-en-1-yl)-4-(1-methyl-6- (morpholine-4-carbonyl)-1H-BENZO[D]IMIDAZOL-4-yl)-1,6-dihydro-7H- PYRROLO[2,3-C]PYRIDIN-7-one)
Analyse TAF1-BD2 in complex with CPD27 (6-(but-3-en-1-yl)-4-(1-methyl-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DF7
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription initiation factor tfiid subunit
- UniProt
- U3KMH2
- Ligands
- G9V
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription initiation factor tfiid subunit | protein | 135 | 72% helix, 0% strand | U3KMH2 |
| B | Transcription initiation factor tfiid subunit | protein | 121 | 70% helix, 0% strand | U3KMH2 |
Ligands and binding sites
- G9V · 6-(but-3-en-1-yl)-4-[1-methyl-6-(morpholine-4-carbonyl)-1H-benzimidazol-4-yl]-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.65 | 0.78 | 38 | empty |
| 2 | 108 | 0.53 | 0.82 | 21 | G9V |
| 3 | 117 | 0.51 | 0.81 | 22 | G9V |
| 4 | 72 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 573 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6DF7 · TAF1-BD2 in complex with Cpd27 (6-(but-3-en-1-yl)-4-(1-methyl-6-(morpholine-4-carbonyl)-1H… · 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 U3KMH2
- Elsewhere: RCSB PDB 6DF7 · PDBe 6DF7 · UniProt U3KMH2
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