SMTL ID : 6gva.1

CDK2/cyclin A2 in complex with pyrazolo[4,3-d]pyrimidine inhibitor LGR4455

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FCQ: 5-(2-azanylethylsulfanyl)-3-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine(Non-covalent)

FCQ.1: 15 residues within 4Å: Chain A: E.9, K.10, I.11, V.19, A.32, F.81, E.82, F.83, L.84, H.85, Q.86, D.87, K.90, Q.132, L.135 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.11, A:I.11, A:V.19, A:A.32, A:F.81, A:F.81, A:F.83, A:L.135 Hydrogen bonds: A:E.82, A:L.84, A:L.84, A:Q.132

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

EDO.2: 1 residues within 4Å: Chain A: K.57 No protein-ligand interaction detected (PLIP) EDO.3: 5 residues within 4Å: Chain A: L.149, E.163, V.165, T.166, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.163, A:T.166, A:R.170 EDO.7: 1 residues within 4Å: Chain B: K.205 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 1 residues within 4Å: Chain A: P.255 Ligand excluded by PLIP

1 x BR: BROMIDE ION(Non-covalent)

BR.5: 1 residues within 4Å: Chain A: L.26 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 6 residues within 4Å: Chain B: M.36, I.39, L.40, W.43, R.76, Q.80 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.80

1 x SGM: MONOTHIOGLYCEROL(Non-covalent)

SGM.8: 5 residues within 4Å: Chain B: M.15, K.18, C.19, R.67, D.131 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:E.58, B:D.131

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 5 residues within 4Å: Chain B: D.169, D.171, P.172, K.226, H.230 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jorda, R. et al., 3,5,7-Substituted Pyrazolo[4,3- d]pyrimidine Inhibitors of Cyclin-Dependent Kinases and Their Evaluation in Lymphoma Models. J.Med.Chem. (2019)

Release Date

2019-05-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclin-dependent kinase 2

Cyclin-A2

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