scPDB - 3nun entry

Protein Data Bank Entry:

PDB ID : 3nun

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2010-07-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-phosphoinositide-dependent protein kinase 1
ID:	PDPK1_HUMAN
AC:	O15530
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:	32.640
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.866	469.125

% Hydrophobic	% Polar
53.24	46.76
According to VolSite

Ligand :

HET Code:	JMZ
Formula:	C11H10N6
Molecular weight:	226.237 g/mol
DrugBank ID:	-
Buried Surface Area:	62.71 %
Polar Surface area:	106.5 Å2

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

Mass center Coordinates

X	Y	Z
-42.0767	15.8801	11.8855

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
C2	CB	LEU- 88	4.28	0	Hydrophobic	false
C2	CG1	VAL- 96	4.5	0	Hydrophobic	false
C3	CG2	VAL- 96	3.52	0	Hydrophobic	false
C5	CG1	VAL- 96	4.36	0	Hydrophobic	false
C6	CG2	VAL- 96	4.05	0	Hydrophobic	false
C9	CB	ALA- 109	3.82	0	Hydrophobic	false
N15	NZ	LYS- 111	3.09	168.17	H-Bond (Protein Donor)	false
N13	OE2	GLU- 130	2.99	171.02	H-Bond (Ligand Donor)	false
C5	CD1	LEU- 159	4.15	0	Hydrophobic	false
N14	O	SER- 160	2.89	141.49	H-Bond (Ligand Donor)	false
N12	O	ALA- 162	3.24	131.98	H-Bond (Ligand Donor)	false
N17	N	ALA- 162	2.94	162.68	H-Bond (Protein Donor)	false
C9	CD1	LEU- 212	3.41	0	Hydrophobic	false
N16	OG1	THR- 222	2.87	148.55	H-Bond (Protein Donor)	false
C6	CG2	THR- 222	4.08	0	Hydrophobic	false