scPDB - 1y57 entry

Protein Data Bank Entry:

PDB ID : 1y57

Resolution :1.910 Å

Experimental Method : X-ray

Deposition Date : 2004-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Proto-oncogene tyrosine-protein kinase Src
ID:	SRC_HUMAN
AC:	P12931
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:	26.491
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.236	455.625

% Hydrophobic	% Polar
60.00	40.00
According to VolSite

Ligand :

HET Code:	MPZ
Formula:	C28H30N7O
Molecular weight:	480.584 g/mol
DrugBank ID:	DB04739
Buried Surface Area:	39.24 %
Polar Surface area:	87.47 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
18.3611	35.4421	39.7746

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
C20	CD2	LEU- 273	4.04	0	Hydrophobic	false
C23	CD1	LEU- 273	3.72	0	Hydrophobic	false
C10	CG2	VAL- 281	4.25	0	Hydrophobic	false
C36	CG2	VAL- 281	3.82	0	Hydrophobic	false
C31	CG1	VAL- 281	3.85	0	Hydrophobic	false
C28	CB	ALA- 293	3.49	0	Hydrophobic	false
N24	O	MET- 341	2.83	150.9	H-Bond (Ligand Donor)	false
N26	N	MET- 341	2.98	169.9	H-Bond (Protein Donor)	false
C22	CD2	LEU- 393	4.46	0	Hydrophobic	false
C28	CD1	LEU- 393	3.36	0	Hydrophobic	false
C31	CD1	LEU- 393	4.01	0	Hydrophobic	false
N34	O	HOH- 766	3.23	156.89	H-Bond (Protein Donor)	false