scPDB - 4au8 entry

Protein Data Bank Entry:

PDB ID : 4au8

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-05-14

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
A	100 %

Ligand binding site composition:

B-Factor:	27.828
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.563	371.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	Z3R
Formula:	C11H8N2O2S3
Molecular weight:	296.388 g/mol
DrugBank ID:	-
Buried Surface Area:	69.03 %
Polar Surface area:	137.91 Å2

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

Mass center Coordinates

X	Y	Z
9.08733	28.2112	0.272222

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
S13	CD1	ILE- 10	4.24	0	Hydrophobic	false
N18	O	ILE- 10	2.76	176.27	H-Bond (Ligand Donor)	false
C6	CG1	VAL- 18	4.4	0	Hydrophobic	false
C3	CG2	VAL- 18	3.82	0	Hydrophobic	false
C4	CG1	VAL- 18	3.86	0	Hydrophobic	false
C6	CB	ALA- 31	3.7	0	Hydrophobic	false
C6	CG2	VAL- 64	4.28	0	Hydrophobic	false
C1	CB	PHE- 80	4	0	Hydrophobic	false
O17	N	ASP- 86	3.03	145.27	H-Bond (Protein Donor)	false
C6	CD1	LEU- 133	3.8	0	Hydrophobic	false
S9	CD2	LEU- 133	3.93	0	Hydrophobic	false
C2	CB	ALA- 143	4	0	Hydrophobic	false
N7	O	HOH- 2089	2.78	179.96	H-Bond (Protein Donor)	false