scPDB - 3lq5 entry

Protein Data Bank Entry:

PDB ID : 3lq5

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2010-02-08

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 9
ID:	CDK9_HUMAN
AC:	P50750
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:	91.588
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.513	678.375

% Hydrophobic	% Polar
40.30	59.70
According to VolSite

Ligand :

HET Code:	SLQ
Formula:	C24H29N7O
Molecular weight:	431.533 g/mol
DrugBank ID:	-
Buried Surface Area:	51.51 %
Polar Surface area:	100.78 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
56.3914	-17.6313	-12.9573

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
C4B	CB	ALA- 23	4.02	0	Hydrophobic	false
C2B	CG2	ILE- 25	3.8	0	Hydrophobic	false
C4'	CG2	ILE- 25	3.76	0	Hydrophobic	false
C5'	CB	ILE- 25	3.86	0	Hydrophobic	false
C10	CG1	VAL- 33	4.12	0	Hydrophobic	false
C10	CB	ALA- 46	3.44	0	Hydrophobic	false
C11	CG2	VAL- 79	3.22	0	Hydrophobic	false
C9	CB	PHE- 103	3.97	0	Hydrophobic	false
C10	CD2	PHE- 103	3.5	0	Hydrophobic	false
C11	CG	PHE- 103	4.16	0	Hydrophobic	false
N6	O	CYS- 106	3.04	137.31	H-Bond (Ligand Donor)	false
N7	N	CYS- 106	3.13	155.4	H-Bond (Protein Donor)	false
CA'	CB	ASP- 109	4.24	0	Hydrophobic	false
C11	CD1	LEU- 156	3.87	0	Hydrophobic	false
C11	CB	ALA- 166	4.09	0	Hydrophobic	false
C13	CB	ALA- 166	4.47	0	Hydrophobic	false
C13	CB	ASP- 167	4.3	0	Hydrophobic	false