scPDB - 4kd1 entry

Protein Data Bank Entry:

PDB ID : 4kd1

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2013-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclin-dependent kinase 2
ID:	CDK2_HUMAN
AC:	P24941
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.22

Chains:

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

Ligand binding site composition:

B-Factor:	23.373
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.258	779.625

% Hydrophobic	% Polar
53.25	46.75
According to VolSite

Ligand :

HET Code:	1QK
Formula:	C21H28N6O2
Molecular weight:	396.486 g/mol
DrugBank ID:	-
Buried Surface Area:	73.47 %
Polar Surface area:	91.15 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
55.5598	79.8573	28.0201

Binding mode :

What is Poseview ?

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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
C22	CG2	ILE- 10	4.45	0	Hydrophobic	false
C14	CG2	ILE- 10	4.02	0	Hydrophobic	false
C02	CG1	VAL- 18	4.19	0	Hydrophobic	false
C25	CG2	VAL- 18	3.64	0	Hydrophobic	false
C02	CB	ALA- 31	3.52	0	Hydrophobic	false
O29	NZ	LYS- 33	2.57	154.05	H-Bond (Protein Donor)	false
C01	CG1	VAL- 64	3.93	0	Hydrophobic	false
C01	CG	PHE- 80	3.58	0	Hydrophobic	false
C02	CB	PHE- 80	3.89	0	Hydrophobic	false
N12	O	LEU- 83	2.65	146.84	H-Bond (Ligand Donor)	false
N05	N	LEU- 83	3.24	174.93	H-Bond (Protein Donor)	false
C13	CB	ASP- 86	4.37	0	Hydrophobic	false
C22	CB	ASP- 86	4.25	0	Hydrophobic	false
O20	NZ	LYS- 89	2.99	122.91	H-Bond (Protein Donor)	false
C23	CG	GLN- 131	3.69	0	Hydrophobic	false
C28	CB	ASN- 132	4.09	0	Hydrophobic	false
C01	CD1	LEU- 134	3.99	0	Hydrophobic	false
C28	CB	ALA- 144	4.43	0	Hydrophobic	false
C01	CB	ALA- 144	3.83	0	Hydrophobic	false