scPDB - 1rjd entry

Protein Data Bank Entry:

PDB ID : 1rjd

Resolution :1.800 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
C	100 %

Ligand binding site composition:

B-Factor:	15.195
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.258	1215.000

% Hydrophobic	% Polar
46.39	53.61
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	75.79 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
27.8215	113.244	-39.6598

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
C2'	CG2	ILE- 5	4.43	0	Hydrophobic	false
CE	CB	THR- 8	3.69	0	Hydrophobic	false
SD	CB	ASP- 9	4.22	0	Hydrophobic	false
C3'	CB	ASP- 9	4.22	0	Hydrophobic	false
SD	CB	ALA- 12	4.44	0	Hydrophobic	false
CG	CB	ALA- 12	4.14	0	Hydrophobic	false
O	CZ	ARG- 81	3.96	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 81	2.84	147.84	H-Bond (Protein Donor)	false
N	O	GLY- 105	2.77	166.44	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 128	2.71	166.19	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 128	2.73	162.62	H-Bond (Ligand Donor)	false
C2'	CD1	TYR- 129	4.47	0	Hydrophobic	false
DuAr	DuAr	TYR- 129	3.73	0	Aromatic Face/Face	false
N6	OD1	ASP- 175	3.03	144.45	H-Bond (Ligand Donor)	false
N1	N	LEU- 176	2.96	172.09	H-Bond (Protein Donor)	false
N	O	GLU- 201	2.89	162.9	H-Bond (Ligand Donor)	false
CG	CB	CYS- 202	4.2	0	Hydrophobic	false
CE	CB	CYS- 202	3.8	0	Hydrophobic	false
C1'	CD1	LEU- 203	4.04	0	Hydrophobic	false
CE	CE1	TYR- 206	3.64	0	Hydrophobic	false
C5'	CE1	TYR- 206	4.08	0	Hydrophobic	false
N	O	HOH- 811	2.84	165.96	H-Bond (Ligand Donor)	false