SMTL ID : 9jk1.1 (1 other biounit)

Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

hetero-1-1-mer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x 01: N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide

01.2: 18 residues within 4Å: Chain A: I.21, A.42, K.44, F.101, E.102, Y.103, M.104, D.105, H.106, D.107, G.110, L.111, S.114, L.154, P.322, W.324, Q.325, C.327 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.21, A:A.42, A:Y.103, A:L.111, A:L.154, A:P.322, A:W.324, A:Q.325 Hydrogen bonds: A:M.104, A:M.104, A:H.106, A:D.107, A:D.107 pi-Stacking: A:H.106

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: N.152, D.165 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Discovery of YJZ5118 : A Potent and Highly Selective Irreversible CDK12/13 Inhibitor with Synergistic Effects in Combination with Akt Inhibition. J.Med.Chem. (2025)

Release Date

2025-05-07

Peptides

Cyclin-dependent kinase 12: A
Cyclin-K: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Cyclin-dependent kinase 12

Cyclin-K

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