SMTL ID : 6rij.2 (1 other biounit)

CDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x K4W: 4-[[[5-nitroso-2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-6-(propan-2-ylamino)pyrimidin-4-yl]amino]methyl]phenol(Non-covalent)

K4W.1: 18 residues within 4Å: Chain A: E.9, I.11, E.13, V.19, A.32, V.65, F.81, E.82, F.83, L.84, H.85, Q.86, D.87, K.90, Q.132, N.133, L.135, D.146 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.11, A:V.19, A:V.19, A:V.65, A:F.81, A:F.81, A:F.83 Hydrogen bonds: A:E.9, A:L.84, A:L.84 Water bridges: A:Q.132, A:D.146, A:D.146

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: V.227, H.269, Y.270 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.269, A:Y.270 Water bridges: A:R.246, A:D.271 NA.4: 3 residues within 4Å: Chain B: M.26, Q.29, I.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.26

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: F.153, P.156, V.157, S.182 Chain B: Y.4, H.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.4, A:V.157, A:S.182 GOL.5: 4 residues within 4Å: Chain B: H.9, T.10, K.205, T.206 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.9, B:K.205, B:T.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Skerlova, J. et al., CDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436. To Be Published

Release Date

2020-07-22

Peptides

Cyclin-dependent kinase 2: A
Cyclin-A2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cyclin-dependent kinase 2

Cyclin-A2

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