scPDB - 2bdj entry

Protein Data Bank Entry:

PDB ID : 2bdj

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-10-20

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:	34.786
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.192	479.250

% Hydrophobic	% Polar
59.15	40.85
According to VolSite

Ligand :

HET Code:	HET
Formula:	C26H30N5O2P
Molecular weight:	475.522 g/mol
DrugBank ID:	-
Buried Surface Area:	58.55 %
Polar Surface area:	102.74 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.7124	5.07585	25.0478

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
CS5	CB	LEU- 273	4	0	Hydrophobic	false
CR1	CD2	LEU- 273	3.71	0	Hydrophobic	false
CT0	CG1	VAL- 281	4.28	0	Hydrophobic	false
CS5	CG1	VAL- 281	3.47	0	Hydrophobic	false
CT0	CB	ALA- 293	4	0	Hydrophobic	false
OH	NZ	LYS- 295	3.06	121.45	H-Bond (Protein Donor)	false
DuAr	NZ	LYS- 295	3.91	136.27	Pi/Cation	false
CT6	CD	LYS- 295	4.24	0	Hydrophobic	false
CT3	CB	LYS- 295	3.63	0	Hydrophobic	false
CT4	CD	LYS- 295	3.84	0	Hydrophobic	false
OH	OE2	GLU- 310	2.66	150.04	H-Bond (Ligand Donor)	false
CT4	SD	MET- 314	4.43	0	Hydrophobic	false
C1A	CG1	VAL- 323	4.23	0	Hydrophobic	false
CT3	CG2	ILE- 336	3.61	0	Hydrophobic	false
CT3	CG2	THR- 338	3.53	0	Hydrophobic	false
N7A	N	MET- 341	2.85	163.84	H-Bond (Protein Donor)	false
N6A	O	MET- 341	2.77	129.45	H-Bond (Ligand Donor)	false
CS2	CB	SER- 345	4.25	0	Hydrophobic	false
C1A	CD1	LEU- 393	3.39	0	Hydrophobic	false
CS2	CD2	LEU- 393	4.05	0	Hydrophobic	false
CT6	CB	ALA- 403	4.25	0	Hydrophobic	false
OH	N	ASP- 404	2.94	147.89	H-Bond (Protein Donor)	false