scPDB - 4yvk entry

Protein Data Bank Entry:

PDB ID : 4yvk

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2015-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (guanine-N(1)-)-methyltransferase
ID:	TRMD_HAEIN
AC:	P43912
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	2.1.1.228

Chains:

Chain Name:	Percentage of Residues within binding site
A	76 %
B	24 %

Ligand binding site composition:

B-Factor:	61.258
Number of residues:	38
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.678	698.625

% Hydrophobic	% Polar
49.76	50.24
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	83.16 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
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
-34.622	8.21256	-2.59848

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
O3'	OH	TYR- 86	2.84	144.12	H-Bond (Ligand Donor)	false
O2'	O	LEU- 87	2.72	153.85	H-Bond (Ligand Donor)	false
CB	CG	PRO- 89	4.42	0	Hydrophobic	false
O	NE2	GLN- 90	3.05	164.38	H-Bond (Protein Donor)	false
O2'	N	GLY- 113	2.91	136.48	H-Bond (Protein Donor)	false
NE	O	TYR- 115	2.7	146.74	H-Bond (Ligand Donor)	false
N	O	GLU- 116	2.63	138.27	H-Bond (Ligand Donor)	false
N6	OG	SER- 132	3.35	132.56	H-Bond (Ligand Donor)	false
N1	N	ILE- 133	3.21	160.77	H-Bond (Protein Donor)	false
N6	O	GLY- 134	3.02	131.44	H-Bond (Ligand Donor)	false
N6	O	TYR- 136	2.85	155.12	H-Bond (Ligand Donor)	false
NE	O	LEU- 138	3.1	148.25	H-Bond (Ligand Donor)	false
N7	N	LEU- 138	3.18	164.59	H-Bond (Protein Donor)	false
N	OD2	ASP- 169	3.47	135.22	H-Bond (Ligand Donor)	false
NE	OD2	ASP- 169	2.76	157.2	H-Bond (Ligand Donor)	false
N	OD2	ASP- 169	3.47	0	Ionic (Ligand Cationic)	false
NE	OD2	ASP- 169	2.76	0	Ionic (Ligand Cationic)	false
O	OG	SER- 170	3.42	126.19	H-Bond (Protein Donor)	false
OXT	OG	SER- 170	2.82	151.64	H-Bond (Protein Donor)	false
OXT	N	SER- 170	2.74	152.98	H-Bond (Protein Donor)	false
N	OD2	ASP- 177	2.85	150.91	H-Bond (Ligand Donor)	false
N	OD2	ASP- 177	2.85	0	Ionic (Ligand Cationic)	false