SMTL ID : 8p4z.2 (1 other biounit)

Crystal structure of the human CDK7 kinase domain in complex with LDC4297

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

1 x WZ8: 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine(Non-covalent)

WZ8.1: 13 residues within 4Å: Chain A: L.11, G.12, V.19, A.32, F.84, D.85, F.86, M.87, E.88, T.89, D.90, L.137, A.147 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.11, A:L.11, A:V.19, A:A.32, A:F.84, A:L.137, A:A.147 Hydrogen bonds: A:M.87, A:M.87

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: H.64, P.65, Q.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.116 GOL.3: 6 residues within 4Å: Chain A: T.221, L.222, P.246, G.247, I.248, Q.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.246, A:I.248, A:L.250, A:Q.266 GOL.4: 7 residues within 4Å: Chain A: L.200, L.201, I.253, F.254, S.255, A.256, A.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.254, A:S.255, A:S.255, A:A.256 GOL.5: 5 residues within 4Å: Chain A: E.119, H.122, T.278, A.279, T.280 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.122, A:T.278, A:A.279, A:T.280, A:T.280 GOL.6: 7 residues within 4Å: Chain A: K.108, A.256, A.257, G.258, D.260, L.261, P.292 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.108, A:K.108, A:A.256, A:G.258, A:D.260 GOL.8: 4 residues within 4Å: Chain A: L.201, P.204, F.205, P.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.204

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.7: 8 residues within 4Å: Chain A: R.129, R.181, M.182, Y.183, G.184, V.185, G.186, P.273 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.181, A:Y.183, A:G.184, A:V.185, A:G.186 Water bridges: A:G.184, A:V.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laursen, M. et al., Crystal structure of the human CDK7 kinase domain in complex with LDC4297. To Be Published

Release Date

2023-06-14

Peptides

Cyclin-dependent kinase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cyclin-dependent kinase 7

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