scPDB - 3nup entry

Protein Data Bank Entry:

PDB ID : 3nup

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-07-07

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 6
ID:	CDK6_HUMAN
AC:	Q00534
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:	60.149
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.895	691.875

% Hydrophobic	% Polar
50.73	49.27
According to VolSite

Ligand :

HET Code:	3NU
Formula:	C16H25N6
Molecular weight:	301.410 g/mol
DrugBank ID:	-
Buried Surface Area:	62.35 %
Polar Surface area:	70.92 Å2

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

Mass center Coordinates

X	Y	Z
23.478	35.7111	-8.06909

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
C10	CG2	ILE- 19	4.29	0	Hydrophobic	false
C15	CG2	ILE- 19	3.85	0	Hydrophobic	false
C10	CG2	VAL- 27	3.6	0	Hydrophobic	false
C6	CB	ALA- 41	3.75	0	Hydrophobic	false
N1	NZ	LYS- 43	3.16	137.92	H-Bond (Protein Donor)	false
C6	CB	PHE- 98	4.14	0	Hydrophobic	false
N3	N	VAL- 101	3.27	162.76	H-Bond (Protein Donor)	false
N5	O	VAL- 101	2.83	139.72	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 104	3.67	0	Ionic (Ligand Cationic)	false
C9	CB	ASN- 150	4.22	0	Hydrophobic	false
C6	CD1	LEU- 152	3.92	0	Hydrophobic	false
C12	CD2	LEU- 152	3.5	0	Hydrophobic	false
C6	CB	ALA- 162	4.49	0	Hydrophobic	false