scPDB - 1z5m entry

Protein Data Bank Entry:

PDB ID : 1z5m

Resolution :2.170 Å

Experimental Method : X-ray

Deposition Date : 2005-03-18

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:	23.024
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.685	486.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	LI8
Formula:	C23H31BrN8O3
Molecular weight:	547.448 g/mol
DrugBank ID:	-
Buried Surface Area:	58.34 %
Polar Surface area:	154.37 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-4.2826	43.7281	44.5096

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
C11	CB	LEU- 88	4.02	0	Hydrophobic	false
C27	CB	LEU- 88	4.13	0	Hydrophobic	false
C15	CD2	LEU- 88	3.97	0	Hydrophobic	false
C14	CD2	LEU- 88	4.06	0	Hydrophobic	false
N16	O	LEU- 88	2.85	161.77	H-Bond (Ligand Donor)	false
N39	O	GLY- 89	2.91	125.92	H-Bond (Ligand Donor)	false
O38	OG	SER- 94	3.07	162.1	H-Bond (Protein Donor)	false
C27	CB	VAL- 96	3.75	0	Hydrophobic	false
C1	CG1	VAL- 96	3.92	0	Hydrophobic	false
C1	CB	ALA- 109	3.66	0	Hydrophobic	false
BR7	CG1	VAL- 143	4.09	0	Hydrophobic	false
BR7	CD1	LEU- 159	3.25	0	Hydrophobic	false
N5	N	ALA- 162	2.83	162.17	H-Bond (Protein Donor)	false
N8	O	ALA- 162	2.76	142.01	H-Bond (Ligand Donor)	false
O19	N	GLU- 166	3.41	175.31	H-Bond (Protein Donor)	false
C1	CD1	LEU- 212	3.69	0	Hydrophobic	false
C28	CD2	LEU- 212	4.19	0	Hydrophobic	false
C36	CB	ASP- 223	4.22	0	Hydrophobic	false