MolNFT v1 · #170535 · protein
Crystal structure of ZMCKO4A in complex with inhibitor 1-[2-(2- hydroxy-ethyl)-phenyl]-3-(3-trifluoromethoxy-phenyl)-urea
6YAO · Cytokinin dehydrogenase 4: “Crystal structure of ZMCKO4A in complex with inhibitor 1-[2-(2…”. X-ray diffraction, 2 ligands (FAD, OJ2), 6 pockets (best druggability 0.83). MolNFT v1 #170535 on GenesisL1: 3D structure, binding sites…
- PDB
- 6YAO
- Type
- protein
- Length
- 453 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, OJ2
- Pockets
- 6 · 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 | 453 | 33% helix, 24% strand | E3T1W8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- OJ2 · 1-[2-(2-Hydroxy-ethyl)-phenyl]-3-(3-trifluoromethoxy-phenyl)-urea · ligand · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.83 | 0.84 | 98 | FAD, OJ2, DMS |
| 2 | 107 | 0.44 | 0.79 | 18 | empty |
| 3 | 111 | 0.38 | 0.75 | 19 | empty |
| 4 | 84 | 0.37 | 0.77 | 23 | empty |
| 5 | 62 | 0.37 | 0.79 | 16 | empty |
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 6YAO · 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 6YAO · PDBe 6YAO · UniProt E3T1W8
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