scPDB - 3gub entry

Protein Data Bank Entry:

PDB ID : 3gub

Resolution :1.710 Å

Experimental Method : X-ray

Deposition Date : 2009-03-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Death-associated protein kinase 1
ID:	DAPK1_HUMAN
AC:	P53355
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:	20.001
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.033	607.500

% Hydrophobic	% Polar
52.22	47.78
According to VolSite

Ligand :

HET Code:	GUB
Formula:	C18H21N5O4
Molecular weight:	371.390 g/mol
DrugBank ID:	-
Buried Surface Area:	70.78 %
Polar Surface area:	125.55 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
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
-23.8938	3.8523	-10.4444

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
C14	CB	LEU- 19	4.33	0	Hydrophobic	false
C16	CG2	VAL- 27	4.49	0	Hydrophobic	false
C2	CB	ALA- 40	3.84	0	Hydrophobic	false
C24	CB	LYS- 42	3.88	0	Hydrophobic	false
C25	CD1	LEU- 68	3.72	0	Hydrophobic	false
C26	CG2	ILE- 77	3.84	0	Hydrophobic	false
C2	CG1	ILE- 77	3.58	0	Hydrophobic	false
C27	CG1	ILE- 77	3.43	0	Hydrophobic	false
C25	CD1	LEU- 79	3.9	0	Hydrophobic	false
C24	CB	LEU- 91	3.73	0	Hydrophobic	false
N4	O	GLU- 94	2.79	150.63	H-Bond (Ligand Donor)	false
N6	N	VAL- 96	3.16	164.43	H-Bond (Protein Donor)	false
O22	OE2	GLU- 100	2.65	154.88	H-Bond (Ligand Donor)	false
C21	CG	GLU- 100	4	0	Hydrophobic	false
O20	O	GLU- 143	2.81	169.64	H-Bond (Ligand Donor)	false
C21	SD	MET- 146	3.78	0	Hydrophobic	false
C3	CG2	ILE- 160	4.2	0	Hydrophobic	false
C19	CD1	ILE- 160	3.68	0	Hydrophobic	false