Crystal structure of human KDM2A with substrate competitive inhibitor 183c. Determined by X-ray diffraction at 2.16 Å resolution. Released 1 Jul 2026.
Explore 9PHV in 3D Show helices and sheets RCSB PDB PDBe
9PHV contains 22 α-helices and 18 β-strands across 2 chains. 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 | 40-45 | 6 | |
| β-strand | 50 | 1 | 1 |
| β-strand | 55-56 | 2 | 2 |
| α-helix | 59-61 | 3 | |
| α-helix | 64-70 | 7 | |
| β-strand | 76-78 | 3 | 2 |
| β-strand | 87 | 1 | 3 |
| α-helix | 95-102 | 8 | |
| β-strand | 107-112 | 6 | 2 |
| β-strand | 117-122 | 6 | 2 |
| α-helix | 123-130 | 8 | |
| α-helix | 134-136 | 3 | |
| β-strand | 141-147 | 7 | 2 |
| α-helix | 152-156 | 5 | |
| β-strand | 158 | 1 | 3 |
| α-helix | 161-166 | 6 | |
| α-helix | 168-172 | 5 | |
| α-helix | 175-178 | 4 | |
| β-strand | 199-203 | 5 | 2 |
| β-strand | 208-212 | 5 | 1 |
| α-helix | 215-217 | 3 | |
| β-strand | 219-226 | 8 | 2 |
| β-strand | 229-234 | 6 | 1 |
| α-helix | 238-250 | 13 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-261 | 4 | |
| β-strand | 266-270 | 5 | 1 |
| α-helix | 271 | 1 | |
| β-strand | 275-278 | 4 | 2 |
| β-strand | 283-287 | 5 | 1 |
| β-strand | 292-299 | 8 | 2 |
| α-helix | 305-318 | 14 | |
| α-helix | 322-324 | 3 | |
| α-helix | 329-345 | 17 | |
| β-strand | 350 | 1 | 4 |
| α-helix | 352-363 | 12 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 455-470 | 16 | |
| α-helix | 473-475 | 3 | |
| β-strand | 482 | 1 | 4 |
| α-helix | 485-498 | 14 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Lysine-specific demethylase 2A | A | protein | 383 | Homo sapiens | Q9Y2K7 (AlphaFold model) |
| Lysine-specific demethylase 2A | D | protein | 69 | Homo sapiens | Q9Y2K7 (AlphaFold model) |
>9PHV_1 Lysine-specific demethylase 2A (chains A) GEPEEERIRYSQRLRGTMRRRYEDDGISDDEIEGKRTFDLEEKLHTNKYNANFVTFMEGK DFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIE MTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKES QTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHN LELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFL HSFNIPMQLKIYNIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKEFQKESLS MDLELNGLESGNGDEEAVDREPR
>9PHV_2 Lysine-specific demethylase 2A (chains D) MQVHLTHFELEGLRCLVDKLESLPLHKKCVPTGIEDEDALIADVKILLEELANSDPKLAL TGVPIVQWP
| ID | Name | Formula | Copies |
|---|---|---|---|
| AKG | 2-oxoglutaric acid | C5 H6 O5 | 1 |
| A1CIP | {6-[(3R,4R)-1-cyclobutyl-4-ethylpiperidine-3-carbonyl]-2-methoxynaphthalen-1-yl… | C25 H30 N2 O2 | 1 |
| NI | Nickel (II) ion | Ni | 1 |
Water and common crystallization additives (GOL, TRS, DMS) are not listed.
Structural insights into the selective inhibition of KDM2A by compound 183c. Mader, P., Pau, V.P.T., Mao, D.Y.L. et al. To be published.
Other PDB entries of the same protein (UniProt Q9Y2K7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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