SMTL ID : 6ya6.1

Minimal construct of Cdc7-Dbf4 bound to XL413

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0SX: 8-chloro-2-[(2S)-pyrrolidin-2-yl][1]benzofuro[3,2-d]pyrimidin-4(3H)-one(Non-covalent)

0SX.1: 17 residues within 4Å: Chain A: G.30, E.31, G.32, S.35, V.37, A.53, K.55, M.83, M.99, P.100, Y.101, L.102, H.104, N.147, L.149, V.160, D.161 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.37, A:A.53 Hydrogen bonds: A:N.147, A:D.161 Water bridges: A:N.147, A:D.161, A:F.162 Halogen bonds: A:L.102

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.198, C.200, C.207, C.210 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.200, A:C.207, A:C.210 ZN.5: 4 residues within 4Å: Chain B: C.90, C.93, H.103, H.109 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.90, B:C.93, B:H.103, B:H.109

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 10 residues within 4Å: Chain A: E.31, G.32, T.33, F.34, S.35, S.36, H.56, L.57, I.58, P.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.31, A:E.31

1 x BO3: BORIC ACID(Non-covalent)

BO3.4: 2 residues within 4Å: Chain A: E.49, E.50 No protein-ligand interaction detected (PLIP)

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

CL.6: 2 residues within 4Å: Chain A: K.205 Chain B: R.8 Ligand excluded by PLIP

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 1 residues within 4Å: Chain B: T.31 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dick, S.D. et al., Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase. Structure (2020)

Release Date

2020-05-27

Peptides

Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase: A
Protein DBF4 homolog A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase

Protein DBF4 homolog A

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