scPDB - 1yvj entry

Protein Data Bank Entry:

PDB ID : 1yvj

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2005-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosine-protein kinase JAK3
ID:	JAK3_HUMAN
AC:	P52333
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	21.772
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.362	1177.875

% Hydrophobic	% Polar
50.14	49.86
According to VolSite

Ligand :

HET Code:	4ST
Formula:	C28H31N4O3
Molecular weight:	471.571 g/mol
DrugBank ID:	-
Buried Surface Area:	63.86 %
Polar Surface area:	74.03 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	8
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
8.15911	-12.4665	-5.94809

Binding mode :

What is Poseview ?

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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
CBB	CB	LEU- 828	4.4	0	Hydrophobic	false
CAK	CD1	LEU- 828	4.34	0	Hydrophobic	false
CAZ	CD1	LEU- 828	4.03	0	Hydrophobic	false
CAC	CG2	VAL- 836	4.15	0	Hydrophobic	false
CBA	CG1	VAL- 836	3.83	0	Hydrophobic	false
CAH	CG2	VAL- 836	3.25	0	Hydrophobic	false
CAU	CB	ALA- 853	4.1	0	Hydrophobic	false
CAF	CD	LYS- 855	4.03	0	Hydrophobic	false
CAE	SD	MET- 902	4	0	Hydrophobic	false
CAG	CE	MET- 902	3.5	0	Hydrophobic	false
NAP	O	GLU- 903	2.91	123.84	H-Bond (Ligand Donor)	false
CAK	CE1	TYR- 904	3.99	0	Hydrophobic	false
OAD	N	LEU- 905	2.88	178.19	H-Bond (Protein Donor)	false
NAO	O	ARG- 953	2.93	140.85	H-Bond (Ligand Donor)	false
CAB	CD2	LEU- 956	3.96	0	Hydrophobic	false
CBB	CD2	LEU- 956	4.38	0	Hydrophobic	false
CAU	CD1	LEU- 956	3.5	0	Hydrophobic	false
CAW	CD1	LEU- 956	3.25	0	Hydrophobic	false
CAB	CB	ALA- 966	3.71	0	Hydrophobic	false
CAB	CB	ASP- 967	4.22	0	Hydrophobic	false
CAF	CB	ASP- 967	3.57	0	Hydrophobic	false