scPDB - 3lcc entry

Protein Data Bank Entry:

PDB ID : 3lcc

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-01-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiocyanate methyltransferase 1
ID:	HOL1_ARATH
AC:	Q0WP12
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	5.253
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.732	374.625

% Hydrophobic	% Polar
64.86	35.14
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.1 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-4.05985	28.0178	12.4577

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
C3'	CE3	TRP- 36	3.83	0	Hydrophobic	false
C2'	CB	TRP- 36	3.58	0	Hydrophobic	false
C5'	CZ3	TRP- 36	4.08	0	Hydrophobic	false
O3'	NE1	TRP- 40	2.97	158.2	H-Bond (Protein Donor)	false
SD	CE2	TRP- 47	3.48	0	Hydrophobic	false
CG	CE2	TRP- 47	4.32	0	Hydrophobic	false
N	O	GLY- 74	2.8	155.28	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 95	2.68	172.32	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 95	3.42	124.08	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 95	2.61	158.59	H-Bond (Ligand Donor)	false
N3	N	ILE- 96	3.43	143.24	H-Bond (Protein Donor)	false
N6	OD1	ASP- 123	2.81	156.32	H-Bond (Ligand Donor)	false
N1	N	VAL- 124	3.14	170.9	H-Bond (Protein Donor)	false
CG	CG1	VAL- 140	3.7	0	Hydrophobic	false
C1'	CE1	PHE- 141	4.42	0	Hydrophobic	false
C5'	CB	ALA- 144	3.97	0	Hydrophobic	false
OXT	O	HOH- 236	2.8	179.97	H-Bond (Protein Donor)	false
O	O	HOH- 240	2.76	143.74	H-Bond (Protein Donor)	false