Linked KDM5A Jmj Domain Bound to the Inhibitor N11 [3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyridine-4-carboxylic acid]. Determined by X-ray diffraction at 1.57 Å resolution. Released 27 Jul 2016.
Explore 5IVJ in 3D Show helices and sheets RCSB PDB PDBe
5IVJ contains 21 α-helices and 16 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 15-17 | 3 | |
| β-strand | 18 | 1 | 1 |
| α-helix | 19-20 | 2 | |
| β-strand | 21-22 | 2 | 2 |
| α-helix | 28-30 | 3 | |
| α-helix | 32-43 | 12 | |
| β-strand | 48-51 | 4 | 2 |
| α-helix | 59-61 | 3 | |
| β-strand | 69-70 | 2 | 3 |
| α-helix | 72 | 1 | |
| β-strand | 73-76 | 4 | 4 |
| α-helix | 358-360 | 3 | |
| β-strand | 361-362 | 2 | 3 |
| α-helix | 363-378 | 16 | |
| α-helix | 382-384 | 3 | |
| α-helix | 387-398 | 12 | |
| β-strand | 406-409 | 4 | 4 |
| β-strand | 410-414 | 5 | 2 |
| α-helix | 415-418 | 4 | |
| α-helix | 433-440 | 8 | |
| α-helix | 445-447 | 3 | |
| α-helix | 451-453 | 3 | |
| β-strand | 470-474 | 5 | 2 |
| β-strand | 479-483 | 5 | 1 |
| α-helix | 486-488 | 3 | |
| β-strand | 490-498 | 9 | 2 |
| β-strand | 501-506 | 6 | 1 |
| α-helix | 508-510 | 3 | |
| α-helix | 511-521 | 11 | |
| α-helix | 524-527 | 4 | |
| α-helix | 531-534 | 4 | |
| α-helix | 542-547 | 6 | |
| β-strand | 553-557 | 5 | 1 |
| α-helix | 558 | 1 | |
| β-strand | 562-565 | 4 | 2 |
| β-strand | 570-575 | 6 | 1 |
| β-strand | 579-586 | 8 | 2 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Lysine-specific demethylase 5A | A | protein | 330 | Homo sapiens | P29375 (AlphaFold model) |
>5IVJ_1 Lysine-specific demethylase 5A (chains A) HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQ PPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYF NMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWG EPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQC AGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
| ID | Name | Formula | Copies |
|---|---|---|---|
| 6ED | 3-({1-[2-(4,4-difluoropiperidin-1-yl)ethyl]-5-fluoro-1H-indazol-3-yl}amino)pyri… | C20 H20 F3 N5 O2 | 1 |
| MN | Manganese (II) ion | Mn | 1 |
Water and common crystallization additives (GOL, DMS) are not listed.
Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Horton, J.R., Liu, X., Gale, M. et al. Cell Chem Biol (2016) 23:769-781. DOI 10.1016/j.chembiol.2016.06.006 · PubMed
Other PDB entries of the same protein (UniProt P29375 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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