scPDB - 4f9a entry

Protein Data Bank Entry:

PDB ID : 4f9a

Resolution :2.170 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:	40.833
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.269	334.125

% Hydrophobic	% Polar
68.69	31.31
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	68.26 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
10.2445	12.9422	29.7482

Binding mode :

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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
O3B	OG	SER- 70	3.22	169.63	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 72	4.41	0	Hydrophobic	false
C5'	CG2	VAL- 72	3.66	0	Hydrophobic	false
O3B	NZ	LYS- 90	3.91	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 90	2.65	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 90	2.65	159.46	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 90	3.03	124.77	H-Bond (Protein Donor)	false
N6	O	PRO- 135	3.11	155.51	H-Bond (Ligand Donor)	false
N1	N	LEU- 137	2.97	167.14	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 139	2.89	167.03	H-Bond (Ligand Donor)	false
O3'	O	SER- 181	2.9	157.71	H-Bond (Ligand Donor)	false
C2'	CD2	LEU- 184	3.84	0	Hydrophobic	false
O1B	MG	MG- 602	2.1	0	Metal Acceptor	false
O2A	MG	MG- 602	1.88	0	Metal Acceptor	false