scPDB - 1rjg entry

Protein Data Bank Entry:

PDB ID : 1rjg

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2003-11-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Leucine carboxyl methyltransferase 1
ID:	LCMT1_YEAST
AC:	Q04081
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.1.1.233

Chains:

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

Ligand binding site composition:

B-Factor:	47.871
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.536	688.500

% Hydrophobic	% Polar
43.14	56.86
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.8 %
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
17.3122	43.8966	31.0825

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
SD	CB	ASP- 9	4.23	0	Hydrophobic	false
C3'	CB	ASP- 9	4.1	0	Hydrophobic	false
CG	CB	ALA- 12	4.04	0	Hydrophobic	false
O	NH2	ARG- 81	3.1	121.61	H-Bond (Protein Donor)	false
O	CZ	ARG- 81	3.95	0	Ionic (Protein Cationic)	false
N	O	GLY- 105	2.8	155.61	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 128	3.33	174.31	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 128	2.53	161.65	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 129	3.79	0	Aromatic Face/Face	false
O2'	OG	SER- 132	3.42	124.5	H-Bond (Protein Donor)	false
N6	OD1	ASP- 175	3.43	146.63	H-Bond (Ligand Donor)	false
N1	N	LEU- 176	3.39	175.59	H-Bond (Protein Donor)	false
N	O	GLU- 201	2.64	122.54	H-Bond (Ligand Donor)	false
N	OE1	GLU- 201	3.79	0	Ionic (Ligand Cationic)	false
CG	CB	CYS- 202	3.98	0	Hydrophobic	false
C1'	CD1	LEU- 203	4.18	0	Hydrophobic	false
C5'	CE1	TYR- 206	4.1	0	Hydrophobic	false