scPDB - 2yx1 entry

Protein Data Bank Entry:

PDB ID : 2yx1

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-04-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (guanine(37)-N1)-methyltransferase Trm5b
ID:	TRM5B_METJA
AC:	Q58293
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	2.1.1.228

Chains:

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

Ligand binding site composition:

B-Factor:	28.410
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.687	810.000

% Hydrophobic	% Polar
49.17	50.83
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	66.34 %
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
61.3837	32.1102	6.68533

Binding mode :

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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
CD	CD2	TYR- 177	3.98	0	Hydrophobic	false
O	CZ	ARG- 186	3.73	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 186	3.08	145.78	H-Bond (Protein Donor)	false
N	O	PHE- 203	2.87	161.78	H-Bond (Ligand Donor)	false
CG	CB	PHE- 203	4.36	0	Hydrophobic	false
C1'	CB	PHE- 203	4.09	0	Hydrophobic	false
C4'	CB	PHE- 203	3.65	0	Hydrophobic	false
O3'	OD2	ASP- 223	2.84	170.17	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 223	2.84	152.18	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 223	3.49	134.11	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 224	4.4	0	Hydrophobic	false
N3	N	ILE- 224	3.38	135.39	H-Bond (Protein Donor)	false
N6	OD1	ASP- 251	3.14	169.93	H-Bond (Ligand Donor)	false
N1	N	VAL- 252	2.81	172.9	H-Bond (Protein Donor)	false
N	OD1	ASN- 265	2.82	155.79	H-Bond (Ligand Donor)	false
NE	O	ASN- 265	3.03	169.2	H-Bond (Ligand Donor)	false
C5'	CD1	LEU- 266	3.64	0	Hydrophobic	false
N	O	HOH- 511	3.28	165.23	H-Bond (Ligand Donor)	false
OXT	O	HOH- 517	2.66	179.95	H-Bond (Protein Donor)	false