scPDB - 4f9c entry

Protein Data Bank Entry:

PDB ID : 4f9c

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2012-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cell division cycle 7-related protein kinase
ID:	CDC7_HUMAN
AC:	O00311
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	34.259
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.941	465.750

% Hydrophobic	% Polar
48.55	51.45
According to VolSite

Ligand :

HET Code:	0SX
Formula:	C14H13ClN3O2
Molecular weight:	290.725 g/mol
DrugBank ID:	DB12357
Buried Surface Area:	74.37 %
Polar Surface area:	71.21 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	2
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
19.8581	18.4557	59.3353

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CL	CD1	ILE- 64	4.03	0	Hydrophobic	false
CAH	CG2	VAL- 72	3.71	0	Hydrophobic	false
CAQ	CG1	VAL- 72	4.01	0	Hydrophobic	false
CL	CB	ALA- 88	4.16	0	Hydrophobic	false
CAC	CB	ALA- 88	3.31	0	Hydrophobic	false
OAA	NZ	LYS- 90	2.72	169.49	H-Bond (Protein Donor)	false
CAD	CE	MET- 118	3.61	0	Hydrophobic	false
CAD	CE	MET- 134	3.73	0	Hydrophobic	false
CL	CD1	TYR- 136	3.49	0	Hydrophobic	false
NAJ	OD1	ASN- 182	2.9	136.54	H-Bond (Ligand Donor)	false
CAM	CD1	LEU- 184	3.49	0	Hydrophobic	false
CAQ	CG1	VAL- 195	4.07	0	Hydrophobic	false
CAD	CG1	VAL- 195	4.07	0	Hydrophobic	false
NAJ	OD2	ASP- 196	3.09	127.82	H-Bond (Ligand Donor)	false
NAJ	OD2	ASP- 196	3.09	0	Ionic (Ligand Cationic)	false