scPDB - 1u59 entry

Protein Data Bank Entry:

PDB ID : 1u59

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2004-07-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.360	7.360	7.360	0.000	7.360	2

List of CHEMBLId :

CHEMBL388978

Binding Site :

Uniprot Annotation

Name:	Tyrosine-protein kinase ZAP-70
ID:	ZAP70_HUMAN
AC:	P43403
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:	50.017
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.201	506.250

% Hydrophobic	% Polar
53.33	46.67
According to VolSite

Ligand :

HET Code:	STU
Formula:	C28H27N4O3
Molecular weight:	467.539 g/mol
DrugBank ID:	DB02010
Buried Surface Area:	65.38 %
Polar Surface area:	74.03 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	2
Rings:	8
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
11.6397	5.15726	53.7921

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
C25	CB	LEU- 344	4.4	0	Hydrophobic	false
C19	CB	LEU- 344	4.29	0	Hydrophobic	false
C4	CD1	LEU- 344	3.82	0	Hydrophobic	false
C20	CB	LEU- 344	3.64	0	Hydrophobic	false
C3	CD2	LEU- 344	4.15	0	Hydrophobic	false
C5	CD1	LEU- 344	3.83	0	Hydrophobic	false
C26	CG2	VAL- 352	3.88	0	Hydrophobic	false
C17	CG2	VAL- 352	3.64	0	Hydrophobic	false
C18	CG1	VAL- 352	4.06	0	Hydrophobic	false
C7	CB	ALA- 367	3.89	0	Hydrophobic	false
C14	CD	LYS- 369	4.19	0	Hydrophobic	false
C13	CE	MET- 414	3.61	0	Hydrophobic	false
N1	O	GLU- 415	2.95	165.94	H-Bond (Ligand Donor)	false
O5	N	ALA- 417	2.63	165.63	H-Bond (Protein Donor)	false
C24	CG	PRO- 421	3.76	0	Hydrophobic	false
C1	CG	PRO- 421	4.35	0	Hydrophobic	false
N4	O	ARG- 465	2.89	130.07	H-Bond (Ligand Donor)	false
C27	CB	ASN- 466	4.34	0	Hydrophobic	false
C27	CD2	LEU- 468	4.34	0	Hydrophobic	false
C5	CD2	LEU- 468	3.98	0	Hydrophobic	false
C7	CD1	LEU- 468	3.32	0	Hydrophobic	false
C27	CB	SER- 478	4.47	0	Hydrophobic	false
C27	CB	ASP- 479	4.22	0	Hydrophobic	false
C15	CB	ASP- 479	3.77	0	Hydrophobic	false