scPDB - 3zdu entry

Protein Data Bank Entry:

PDB ID : 3zdu

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-11-30

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-like 3
ID:	CDKL3_HUMAN
AC:	Q8IVW4
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:	55.892
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
1.137	695.250

% Hydrophobic	% Polar
53.88	46.12
According to VolSite

Ligand :

HET Code:	38R
Formula:	C20H21N7
Molecular weight:	359.428 g/mol
DrugBank ID:	-
Buried Surface Area:	77.08 %
Polar Surface area:	102.31 Å2

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

Mass center Coordinates

X	Y	Z
25.5513	18.9578	60.8741

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
N1I	O	VAL- 10	3.18	139.79	H-Bond (Ligand Donor)	false
C1Y	CG2	VAL- 18	3.97	0	Hydrophobic	false
C03	CG1	VAL- 18	3.86	0	Hydrophobic	false
C1N	CG2	VAL- 18	3.8	0	Hydrophobic	false
C03	CB	ALA- 31	3.43	0	Hydrophobic	false
C1Y	CD	LYS- 33	4.24	0	Hydrophobic	false
N1A	NZ	LYS- 33	2.96	160.31	H-Bond (Protein Donor)	false
C1U	CG2	VAL- 63	4.03	0	Hydrophobic	false
C1U	CG	PHE- 79	3.97	0	Hydrophobic	false
C1T	CB	PHE- 79	3.87	0	Hydrophobic	false
C03	CD1	PHE- 79	3.66	0	Hydrophobic	false
N1Q	O	GLU- 80	2.8	120.76	H-Bond (Ligand Donor)	false
N1P	N	ILE- 82	2.76	152.62	H-Bond (Protein Donor)	false
N1G	O	ILE- 82	2.6	164.74	H-Bond (Ligand Donor)	false
C5	CG2	THR- 85	4.28	0	Hydrophobic	false
C1K	CG2	THR- 85	4.02	0	Hydrophobic	false
C1L	CG	GLU- 129	4.08	0	Hydrophobic	false
C1U	CD1	LEU- 132	4.09	0	Hydrophobic	false
C1K	CD2	LEU- 132	3.91	0	Hydrophobic	false
C1U	CB	CYS- 142	3.93	0	Hydrophobic	false
C1L	SG	CYS- 142	3.97	0	Hydrophobic	false
C01	SG	CYS- 142	3.99	0	Hydrophobic	false
C1V	CB	ASP- 143	4.24	0	Hydrophobic	false
N1I	O	HOH- 2004	2.81	124.49	H-Bond (Ligand Donor)	false