Research workbench
Crystal structure of ZMCKO4A in complex with inhibitor 1-(3-chloro-5- trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea
Analyse Crystal structure of ZMCKO4A in complex with inhibitor 1-(3-chloro-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YAP
- Type
- protein
- Length
- 451 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytokinin dehydrogenase 4
- EC
- 1.5.99.12
- UniProt
- E3T1W8
- Ligands
- FAD, OHZ
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytokinin dehydrogenase 4 (EC 1.5.99.12) | protein | 451 | 33% helix, 24% strand | E3T1W8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- OHZ · 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.83 | 0.87 | 69 | FAD, OHZ |
| 2 | 152 | 0.47 | 0.77 | 22 | empty |
| 3 | 112 | 0.41 | 0.76 | 15 | DMS |
| 4 | 93 | 0.41 | 0.78 | 17 | empty |
| 5 | 82 | 0.38 | 0.77 | 23 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 6YAP · Crystal structure of ZmCKO4a in complex with inhibitor… · 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 E3T1W8
- Elsewhere: RCSB PDB 6YAP · PDBe 6YAP · UniProt E3T1W8
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