scPDB - 5bsm entry

Protein Data Bank Entry:

PDB ID : 5bsm

Resolution :2.320 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
B	100 %

Ligand binding site composition:

B-Factor:	28.055
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.871	975.375

% Hydrophobic	% Polar
40.14	59.86
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	77.91 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.1927	2.84313	-48.6274

Binding mode :

What is Poseview ?

2D View
3D View

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
O3G	OG	SER- 189	2.69	139.65	H-Bond (Protein Donor)	false
O1A	OG	SER- 190	2.51	164.4	H-Bond (Protein Donor)	false
O3A	N	SER- 190	3.21	155.59	H-Bond (Protein Donor)	false
O3G	N	GLY- 191	3.03	131.17	H-Bond (Protein Donor)	false
O1B	OG1	THR- 192	2.8	170.28	H-Bond (Protein Donor)	false
O3B	N	THR- 192	3.19	159.9	H-Bond (Protein Donor)	false
O1G	OG1	THR- 193	2.9	166.4	H-Bond (Protein Donor)	false
O1G	N	THR- 193	2.96	151.89	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 197	3.34	158.7	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 197	3.34	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 197	3.55	0	Ionic (Protein Cationic)	false
N6	OE1	GLN- 331	3.3	163.23	H-Bond (Ligand Donor)	false
N6	O	GLY- 332	2.97	146.65	H-Bond (Ligand Donor)	false
C2'	CE1	TYR- 333	4	0	Hydrophobic	false
C5'	CB	MET- 335	4.09	0	Hydrophobic	false
C3'	CB	MET- 335	4	0	Hydrophobic	false
O2A	N	THR- 336	2.94	164.12	H-Bond (Protein Donor)	false
O2A	OG1	THR- 336	2.66	152.46	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 420	3.28	137.54	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 420	2.56	161.88	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 420	2.67	165.78	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 420	3.39	127.18	H-Bond (Ligand Donor)	false
O1B	CZ	ARG- 435	3.78	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 435	3.75	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 435	2.95	145.96	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 435	2.89	177.3	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 526	3.55	0	Ionic (Protein Cationic)	false
O5'	NZ	LYS- 526	3.12	143.93	H-Bond (Protein Donor)	false
O4'	NZ	LYS- 526	3.23	139.11	H-Bond (Protein Donor)	false
O2G	MG	MG- 601	1.97	0	Metal Acceptor	false
O2B	MG	MG- 601	2.22	0	Metal Acceptor	false