scPDB - 3nax entry

Protein Data Bank Entry:

PDB ID : 3nax

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2010-06-02

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:	15.925
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.443	651.375

% Hydrophobic	% Polar
60.62	39.38
According to VolSite

Ligand :

HET Code:	MP7
Formula:	C28H22F2N4O4
Molecular weight:	516.495 g/mol
DrugBank ID:	-
Buried Surface Area:	79.01 %
Polar Surface area:	99.77 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
7.59526	-4.57321	6.73008

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
C27	CB	SER- 92	4.44	0	Hydrophobic	false
C28	CB	SER- 94	3.66	0	Hydrophobic	false
C22	CG2	VAL- 96	4.03	0	Hydrophobic	false
C29	CG2	VAL- 96	4.02	0	Hydrophobic	false
C17	CG2	VAL- 96	4.03	0	Hydrophobic	false
C13	CG1	VAL- 96	4.16	0	Hydrophobic	false
C14	CB	ALA- 109	3.75	0	Hydrophobic	false
O34	NZ	LYS- 111	2.68	158.58	H-Bond (Protein Donor)	false
C24	CD	LYS- 111	3.59	0	Hydrophobic	false
C26	CG	PRO- 125	3.7	0	Hydrophobic	false
C7	CB	MET- 134	4.03	0	Hydrophobic	false
C8	SD	MET- 134	3.9	0	Hydrophobic	false
C7	CD1	LEU- 137	4.19	0	Hydrophobic	false
F	CE1	PHE- 142	3.36	0	Hydrophobic	false
C5	CB	PHE- 142	4.35	0	Hydrophobic	false
C11	CB	PHE- 142	4.34	0	Hydrophobic	false
C5	CG2	VAL- 143	3.81	0	Hydrophobic	false
C14	CG1	VAL- 143	4.37	0	Hydrophobic	false
C15	CG2	VAL- 143	4.21	0	Hydrophobic	false
C22	CD1	LEU- 159	4.27	0	Hydrophobic	false
C15	CD1	LEU- 159	3.96	0	Hydrophobic	false
N20	O	SER- 160	2.82	176.12	H-Bond (Ligand Donor)	false
O31	N	ALA- 162	2.82	176.27	H-Bond (Protein Donor)	false
F	CD2	LEU- 196	3.94	0	Hydrophobic	false
F12	CD2	LEU- 196	3.37	0	Hydrophobic	false
C9	CD1	LEU- 196	3.87	0	Hydrophobic	false
F12	CG2	ILE- 201	3.74	0	Hydrophobic	false
F12	CB	HIS- 203	4.33	0	Hydrophobic	false
C13	CD1	LEU- 212	3.77	0	Hydrophobic	false
F	CG2	ILE- 221	3.39	0	Hydrophobic	false
C16	CG2	THR- 222	3.78	0	Hydrophobic	false
O	N	ASP- 223	2.99	157.68	H-Bond (Protein Donor)	false
C8	CB	ASP- 223	3.62	0	Hydrophobic	false
C22	CE1	PHE- 224	4.25	0	Hydrophobic	false
C28	CB	PHE- 224	4.47	0	Hydrophobic	false
C17	CZ	PHE- 224	3.43	0	Hydrophobic	false
C8	CB	ALA- 227	3.82	0	Hydrophobic	false