scPDB - 5bsr entry

Protein Data Bank Entry:

PDB ID : 5bsr

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2015-06-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	4-coumarate--CoA ligase 2
ID:	4CL2_TOBAC
AC:	O24146
Organism:	Nicotiana tabacum
Reign:	Eukaryota
TaxID:	4097
EC Number:	6.2.1.12

Chains:

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

Ligand binding site composition:

B-Factor:	17.659
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	AMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.026	634.500

% Hydrophobic	% Polar
58.51	41.49
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	44.26 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
71.9486	17.631	22.7413

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
C1B	CD2	LEU- 110	3.99	0	Hydrophobic	false
C6P	CG	PRO- 234	3.8	0	Hydrophobic	false
C2P	CB	HIS- 237	4.34	0	Hydrophobic	false
C2P	CB	TYR- 239	3.32	0	Hydrophobic	false
S1P	CD1	TYR- 239	3.63	0	Hydrophobic	false
O5A	NZ	LYS- 260	3.06	132.7	H-Bond (Protein Donor)	false
O5A	NZ	LYS- 260	3.06	0	Ionic (Protein Cationic)	false
CEP	CB	PHE- 261	3.75	0	Hydrophobic	false
CDP	CG2	VAL- 281	3.66	0	Hydrophobic	false
CDP	CB	PRO- 283	3.76	0	Hydrophobic	false
CDP	CG1	ILE- 284	4.09	0	Hydrophobic	false
S1P	CB	ALA- 309	3.4	0	Hydrophobic	false
O1A	NZ	LYS- 443	2.97	164.25	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 443	2.97	0	Ionic (Protein Cationic)	false
N8P	O	LYS- 443	3.04	130.73	H-Bond (Ligand Donor)	false
N4P	O	GLY- 444	2.99	120.83	H-Bond (Ligand Donor)	false
CAP	CE2	PHE- 445	4.3	0	Hydrophobic	false
C6P	CZ	PHE- 445	3.55	0	Hydrophobic	false
C1B	CD2	PHE- 506	3.71	0	Hydrophobic	false
C2B	CG	PHE- 506	4.48	0	Hydrophobic	false
C4B	CE1	PHE- 506	3.92	0	Hydrophobic	false
C5B	CZ	PHE- 506	4.39	0	Hydrophobic	false