MolNFT v1 · #168199 · protein
Ternary complex structure - btk ciap compound 15
6W8I · Tyrosine-protein kinase btk: “Ternary complex structure - btk ciap compound 15”. X-ray diffraction, 2 ligands (TKY, ZN), 11 pockets (best druggability 0.78). MolNFT v1 #168199 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6W8I
- Type
- protein
- Length
- 1,044 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase btk; Baculoviral iap repeat-containing protein 2
- EC
- 2.7.10.2, 2.3.2.27
- UniProt
- Q06187, Q13490
- Ligands
- TKY, ZN
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 254 | 38% helix, 18% strand | Q06187 |
| B | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 251 | 37% helix, 17% strand | Q06187 |
| C | Tyrosine-protein kinase btk (EC 2.7.10.2) | protein | 263 | 38% helix, 18% strand | Q06187 |
| D | Baculoviral iap repeat-containing protein 2 (EC 2.3.2.27) | protein | 92 | 42% helix, 8% strand | Q13490 |
| E | Baculoviral iap repeat-containing protein 2 (EC 2.3.2.27) | protein | 93 | 45% helix, 9% strand | Q13490 |
| F | Baculoviral iap repeat-containing protein 2 (EC 2.3.2.27) | protein | 91 | 42% helix, 8% strand | Q13490 |
Ligands and binding sites
- TKY · 14-{[(3S)-2-(N-methyl-L-alanyl-3-methyl-L-valyl)-3-{[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}-1, 2,3,4-tetrahydroisoquinolin-7-yl]oxy}-3,6,9,12-tetraoxatetradecan-1-yl (3R)-3-{5-amino-4-carbamoyl-3-[4-(2,4-difluorophenoxy)phenyl]-1H-pyrazol-1-yl}piperidine-1-carboxylate · ligand · 3 copies · chains C, F, A, D, B, E
- ZN · Zinc ion · metal · 3 copies · chains D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.78 | 0.80 | 108 | empty |
| 2 | 476 | 0.74 | 0.83 | 57 | TKY |
| 3 | 362 | 0.72 | 0.83 | 46 | empty |
| 4 | 438 | 0.58 | 0.74 | 38 | TKY |
| 5 | 232 | 0.53 | 0.77 | 30 | empty |
Interfaces
8 interfaces between chains.
- A–C · 520 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 390 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 368 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 331 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 240 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6W8I · Ternary complex structure - BTK cIAP compound 15 · the same entry in another collection · chain F against F, TM-score 1.00
- Q13490 · AlphaFold monomer V2.0 prediction for baculoviral iap repeat- containing protein 2… · a predicted model of the same protein · chain D against A, TM-score 0.99
- Q06187 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase btk (Q06187) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q06187
- Every structure of UniProt Q13490
- Elsewhere: RCSB PDB 6W8I · PDBe 6W8I · UniProt Q06187 · UniProt Q13490
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