scPDB - 3lpb entry

Protein Data Bank Entry:

PDB ID : 3lpb

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-02-05

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 JAK2
ID:	JAK2_HUMAN
AC:	O60674
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.699
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.147	1140.750

% Hydrophobic	% Polar
46.75	53.25
According to VolSite

Ligand :

HET Code:	NVB
Formula:	C24H23N3O5S
Molecular weight:	465.522 g/mol
DrugBank ID:	-
Buried Surface Area:	58.17 %
Polar Surface area:	108.02 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
77.2793	111.291	21.2667

Binding mode :

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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
O47	O	HOH- 122	3.03	179.94	H-Bond (Protein Donor)	false
C13	CB	LEU- 855	4.18	0	Hydrophobic	false
C34	CD1	LEU- 855	4.08	0	Hydrophobic	false
C35	CB	LEU- 855	4.06	0	Hydrophobic	false
C40	CD2	LEU- 855	3.8	0	Hydrophobic	false
C13	CB	VAL- 863	3.59	0	Hydrophobic	false
C15	CG2	VAL- 863	3.92	0	Hydrophobic	false
C20	CG1	VAL- 863	4.04	0	Hydrophobic	false
C11	CG2	VAL- 863	3.68	0	Hydrophobic	false
C28	CB	ALA- 880	3.34	0	Hydrophobic	false
C30	CG2	VAL- 911	3.81	0	Hydrophobic	false
C30	CE	MET- 929	3.74	0	Hydrophobic	false
C43	CZ	TYR- 931	4	0	Hydrophobic	false
N26	N	LEU- 932	3.03	172.06	H-Bond (Protein Donor)	false
C53	CB	SER- 936	4.48	0	Hydrophobic	false
C15	CD2	LEU- 983	4.42	0	Hydrophobic	false
C20	CD1	LEU- 983	3.71	0	Hydrophobic	false
C28	CD1	LEU- 983	3.68	0	Hydrophobic	false
C35	CD2	LEU- 983	4.35	0	Hydrophobic	false
C18	CB	ASP- 994	4.12	0	Hydrophobic	false