Research workbench
Crystal structure of nik with 11-bromo-5,6,7,8-TETRAHYDROPYRIMIDO[4', 5':3,4]CYCLOHEPTA[1,2-B]INDOL-2-amine (T28)
Analyse Crystal structure of nik with 11-bromo-5,6,7,8-TETRAHYDROPYRIMIDO[4'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IDT
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitogen-activated protein kinase kinase kinase 14
- EC
- 2.7.11.25
- UniProt
- Q99558
- Ligands
- T28
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) | protein | 334 | 35% helix, 19% strand | Q99558 |
| B | Mitogen-activated protein kinase kinase kinase 14 (EC 2.7.11.25) | protein | 335 | 34% helix, 19% strand | Q99558 |
Ligands and binding sites
- T28 · 11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.77 | 0.80 | 81 | T28 |
| 2 | 916 | 0.77 | 0.80 | 82 | T28 |
| 3 | 56 | 0.68 | 0.96 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1468 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4IDT · Crystal Structure of NIK with 11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q99558 · AlphaFold monomer V2.0 prediction for mitogen-activated protein kinase kinase kinase 14… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q99558
- Elsewhere: RCSB PDB 4IDT · PDBe 4IDT · UniProt Q99558
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