MolNFT v1 · #119553 · protein
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 3-methyl-N-pyridin-4-yl-1,2-oxazole-5-carboxamide (N09954A) (ligand modelled based on pandda event MAP, sgc - diamond I04-1 fragment screening)
5FZL · Lysine-specific demethylase 5B: “Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment…”. X-ray diffraction, 5 ligands (UOI, ZN, MN), 6 pockets (best druggability 0.82). MolNFT v1 #119553 on…
- PDB
- 5FZL
- Type
- protein
- Length
- 452 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 5B
- EC
- 1.14.11.-
- UniProt
- Q9UGL1
- Ligands
- UOI, ZN, MN, CL, PO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 5B (EC 1.14.11.-) | protein | 452 | 37% helix, 20% strand | Q9UGL1 |
Ligands and binding sites
- UOI · 3-methyl-N-(pyridin-4-yl)-1,2-oxazole-5-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.82 | 0.84 | 75 | DMS, MN, EDO, UOI |
| 2 | 191 | 0.74 | 0.90 | 25 | EDO |
| 3 | 54 | 0.45 | 0.84 | 19 | empty |
| 4 | 112 | 0.43 | 0.77 | 27 | empty |
| 5 | 56 | 0.36 | 0.78 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FZL · Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UGL1 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 5B (Q9UGL1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9UGL1
- Elsewhere: RCSB PDB 5FZL · PDBe 5FZL · UniProt Q9UGL1
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