Crystal structure of selective inhibitor 16 bound at the active site of CDK1. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Jul 2026.
Explore 11GY in 3D Show helices and sheets RCSB PDB PDBe
11GY contains 42 α-helices and 17 β-strands across 3 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 |
|---|---|---|---|
| β-strand | 4-11 | 8 | 1 |
| β-strand | 16-23 | 8 | 1 |
| β-strand | 29-35 | 7 | 1 |
| α-helix | 46-57 | 12 | |
| β-strand | 63 | 1 | 2 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-72 | 7 | 1 |
| β-strand | 75-81 | 7 | 1 |
| β-strand | 85-86 | 2 | 2 |
| α-helix | 87-93 | 7 | |
| α-helix | 95 | 1 | |
| α-helix | 102-121 | 20 | |
| β-strand | 124-125 | 2 | 3 |
| α-helix | 131-133 | 3 | |
| β-strand | 134-136 | 3 | 2 |
| β-strand | 142-144 | 3 | 2 |
| β-strand | 151-152 | 2 | 3 |
| α-helix | 167-169 | 3 | |
| α-helix | 172-175 | 4 | |
| α-helix | 184-199 | 16 | |
| α-helix | 209-220 | 12 | |
| α-helix | 231-233 | 3 | |
| α-helix | 249-252 | 4 | |
| α-helix | 258-267 | 10 | |
| α-helix | 276-277 | 2 | |
| α-helix | 278-281 | 4 | |
| α-helix | 285-287 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 167-169 | 3 | |
| α-helix | 170-183 | 14 | |
| α-helix | 198-215 | 18 | |
| α-helix | 219-233 | 15 | |
| α-helix | 240-242 | 3 | |
| α-helix | 243-258 | 16 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-270 | 6 | |
| α-helix | 278-291 | 14 | |
| α-helix | 298-300 | 3 | |
| α-helix | 301-311 | 11 | |
| α-helix | 316-328 | 13 | |
| α-helix | 329-331 | 3 | |
| α-helix | 333-335 | 3 | |
| α-helix | 340-355 | 16 | |
| α-helix | 362-368 | 7 | |
| α-helix | 376-391 | 16 | |
| α-helix | 398-402 | 5 | |
| α-helix | 406-408 | 3 | |
| α-helix | 411-413 | 3 | |
| α-helix | 415-418 | 4 | |
| α-helix | 420-426 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-3 | 2 | 4 |
| β-strand | 6-8 | 3 | 4 |
| α-helix | 9-11 | 3 | |
| β-strand | 12-13 | 2 | 4 |
| β-strand | 17-23 | 7 | 4 |
| α-helix | 26-29 | 4 | |
| α-helix | 37-39 | 3 | |
| α-helix | 40-46 | 7 | |
| β-strand | 55-58 | 4 | 4 |
| β-strand | 66-72 | 7 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Cyclin-dependent kinase 1 | A | protein | 316 | Homo sapiens | P06493 (AlphaFold model) |
| G2/mitotic-specific cyclin-B1 | B | protein | 273 | Homo sapiens | P14635 (AlphaFold model) |
| Cyclin-dependent kinases regulatory subunit 2 | C | protein | 80 | Homo sapiens | P33552 (AlphaFold model) |
>11GY_1 Cyclin-dependent kinase 1 (chains A) MHHHHHHGENLYFQGSLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEE EGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMD SSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYT HEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALG TPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMA LNHPYFNDLDNQIKKM
>11GY_2 G2/mitotic-specific cyclin-B1 (chains B) GSHMNLSSEYVKDIYAYLRQLEEEQAVRPKYLLGREVTGNMRAILIDWLVQVQMKFRLLQ ETMYMTVSIIDRFMQNNSVPKKMLQLVGVTAMFIASKYEEMYPPEIGDFAFVTDNTYTKH QIRQMEMKILRALNFGLGRPLPLHFLRRASKIGEVDVEQHTLAKYLMELTMLDYDMVHFP PSQIAAGAFSLALKILDNGEWTPTLQHYLSYTEESLLPVMQHLAKNVVMVNQGLTKHMTV KNKYATSKHAKISTLPQLNSALVQDLAKAVAKV
>11GY_3 Cyclin-dependent kinases regulatory subunit 2 (chains C) GSAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMI HEPEPHILLFRRPLPKDQQK
| ID | Name | Formula | Copies |
|---|---|---|---|
| A1DEQ | (1R,3S)-3-{3-[(1-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)amino]-1H-pyrazol-5-yl}… | C19 H24 N6 O3 | 1 |
| A1DJL | (6S,9R,13S)-6,9-dimethyl-2,5,8,11-tetraoxatetradecan-13-amine | C12 H27 N O4 | 1 |
Water and common crystallization additives (SO4, DMS, EPE, GOL) are not listed.
Utilizing Molecular Dynamics and Mechanistic Pharmacokinetic Studies in the Design of Selective CDK2 Inhibitors. Verma, V.A., Grandner, J.M., Parr, B.T. et al. J Med Chem (2026) 69:15294-15316. DOI 10.1021/acs.jmedchem.5c03803 · PubMed
Other PDB entries of the same protein (UniProt P06493 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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