Linked KDM5A Jmj Domain Bound to the Inhibitor N10 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol. Determined by X-ray diffraction at 1.68 Å resolution. Released 27 Jul 2016.
Explore 5IVF in 3D Show helices and sheets RCSB PDB PDBe
5IVF contains 22 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 | 348-349 | 2 | |
| 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 | |
| α-helix | 455-459 | 5 | |
| 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 | 501-505 | 5 | 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 | 571-575 | 5 | 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) |
>5IVF_1 Lysine-specific demethylase 5A (chains A) HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQ PPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYF NMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWG EPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQC AGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
| ID | Name | Formula | Copies |
|---|---|---|---|
| 6EB | 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4… | C15 H14 F3 N5 O2 | 1 |
| MN | Manganese (II) ion | Mn | 1 |
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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