scPDB - 3o0g entry

Protein Data Bank Entry:

PDB ID : 3o0g

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2010-07-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cyclin-dependent-like kinase 5
ID:	CDK5_HUMAN
AC:	Q00535
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	53.893
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.088	472.500

% Hydrophobic	% Polar
60.71	39.29
According to VolSite

Ligand :

HET Code:	3O0
Formula:	C16H11ClN4O3S
Molecular weight:	374.802 g/mol
DrugBank ID:	-
Buried Surface Area:	59.86 %
Polar Surface area:	142.07 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-5.94944	60.1707	60.8539

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
SAQ	CD1	ILE- 10	4.12	0	Hydrophobic	false
CAT	CD1	ILE- 10	3.89	0	Hydrophobic	false
CAM	CG1	VAL- 18	4.19	0	Hydrophobic	false
CAO	CG1	VAL- 18	3.77	0	Hydrophobic	false
OAW	NZ	LYS- 33	3.92	0	Ionic (Protein Cationic)	false
OAY	NZ	LYS- 33	3.2	0	Ionic (Protein Cationic)	false
NAA	O	GLU- 81	2.7	144.08	H-Bond (Ligand Donor)	false
NAI	N	CYS- 83	3.3	162.41	H-Bond (Protein Donor)	false
NAS	O	CYS- 83	2.81	137.84	H-Bond (Ligand Donor)	false
CAK	CB	GLN- 85	4.45	0	Hydrophobic	false
CAV	CB	ASP- 86	4.15	0	Hydrophobic	false
CLA	CD	LYS- 89	3.77	0	Hydrophobic	false
CAD	CD2	LEU- 133	4.37	0	Hydrophobic	false
SAQ	CD2	LEU- 133	3.96	0	Hydrophobic	false
CAU	CD2	LEU- 133	4.23	0	Hydrophobic	false
CAE	CB	ALA- 143	4.36	0	Hydrophobic	false
CAO	CB	ASN- 144	4.43	0	Hydrophobic	false
CAM	CB	ASN- 144	3.72	0	Hydrophobic	false