LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N44 i.e. 3-((2-(pyridin-2-yl)-6-(4-(vinylsulfonyl)-1,4-diazepan-1-yl)pyrimidin-4-yl)amino)propanoic acid. Determined by X-ray diffraction at 1.59 Å resolution. Released 21 Nov 2018.
Explore 6DQ6 in 3D Show helices and sheets RCSB PDB PDBe
6DQ6 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 | 79 | 1 | |
| α-helix | 80-84 | 5 | |
| 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 | 433-435 | 3 | |
| α-helix | 436-439 | 4 | |
| 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 | 501-505 | 5 | 1 |
| α-helix | 508-510 | 3 | |
| α-helix | 511-521 | 11 | |
| α-helix | 524-526 | 3 | |
| α-helix | 531-534 | 4 | |
| α-helix | 542-547 | 6 | |
| β-strand | 553-557 | 5 | 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 |
|---|---|---|---|---|---|
| Linked KDM5A Jmj Domain | A | protein | 330 | Homo sapiens | P29375 (AlphaFold model) |
>6DQ6_1 Linked KDM5A Jmj Domain (chains A) HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQ PPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYF NMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWG EPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQC AGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
| ID | Name | Formula | Copies |
|---|---|---|---|
| H6J | N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-be… | C19 H24 N6 O4 S | 1 |
| MN | Manganese (II) ion | Mn | 1 |
Water and common crystallization additives (GOL, DMS) are not listed.
Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. Horton, J.R., Woodcock, C.B., Chen, Q. et al. J Med Chem (2018) 61:10588-10601. DOI 10.1021/acs.jmedchem.8b01219 · 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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