LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1l2-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N40). Determined by X-ray diffraction at 1.59 Å resolution. Released 28 Mar 2018.
Explore 6BGV in 3D Show helices and sheets RCSB PDB PDBe
6BGV 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 | 32-43 | 12 | |
| β-strand | 48-51 | 4 | 2 |
| α-helix | 52-54 | 3 | |
| α-helix | 59-61 | 3 | |
| β-strand | 69-70 | 2 | 3 |
| α-helix | 72 | 1 | |
| β-strand | 73-76 | 4 | 4 |
| α-helix | 81-83 | 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 | 433-435 | 3 | |
| α-helix | 436-439 | 4 | |
| α-helix | 445-447 | 3 | |
| α-helix | 456-459 | 4 | |
| 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 |
| 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, linked KDM5A JMJ domain | A | protein | 330 | Homo sapiens | P29375 (AlphaFold model) |
>6BGV_1 Lysine-specific demethylase 5A, linked KDM5A JMJ domain (chains A) HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQ PPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYF NMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWG EPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQC AGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
| ID | Name | Formula | Copies |
|---|---|---|---|
| MN | Manganese (II) ion | Mn | 1 |
| DQG | 2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyrid… | C22 H24 Cl N3 O3 | 1 |
Water and common crystallization additives (EDO, DMS, GOL) are not listed.
Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. Horton, J.R., Liu, X., Wu, L. et al. J Med Chem (2018) 61:3193-3208. DOI 10.1021/acs.jmedchem.8b00261 · 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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