scPDB - 3a4t entry

Protein Data Bank Entry:

PDB ID : 3a4t

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-07-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA (cytosine(48)-C(5))-methyltransferase
ID:	TRM4_METJA
AC:	Q60343
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	2.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	22.902
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.112	712.125

% Hydrophobic	% Polar
31.75	68.25
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	76.1 %
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
20.9726	-23.6987	-10.2673

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
N	O	CYS- 91	3.02	148.24	H-Bond (Ligand Donor)	false
C4'	CB	CYS- 91	4.14	0	Hydrophobic	false
C1'	CB	CYS- 91	3.84	0	Hydrophobic	false
O	NZ	LYS- 97	2.86	174.72	H-Bond (Protein Donor)	false
O	N	LYS- 97	2.96	157.77	H-Bond (Protein Donor)	false
O	NZ	LYS- 97	2.86	0	Ionic (Protein Cationic)	false
O3'	OE1	GLU- 115	2.64	150.62	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 115	3.24	135.58	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 115	3.39	135.93	H-Bond (Ligand Donor)	false
N3	N	ILE- 116	3.03	150.53	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 116	4.48	0	Hydrophobic	false
C3'	CD	ARG- 120	4.07	0	Hydrophobic	false
N6	OD1	ASP- 142	3.21	129.98	H-Bond (Ligand Donor)	false
N1	N	MET- 143	3.28	164.04	H-Bond (Protein Donor)	false
N	OD2	ASP- 163	2.69	145.74	H-Bond (Ligand Donor)	false
N	OD2	ASP- 163	2.69	0	Ionic (Ligand Cationic)	false
C5'	CB	PRO- 165	3.88	0	Hydrophobic	false
NE	OD1	ASN- 169	3.28	149.42	H-Bond (Ligand Donor)	false
N7	NE	ARG- 189	2.9	154.39	H-Bond (Protein Donor)	false
N7	NH2	ARG- 189	3.05	142.45	H-Bond (Protein Donor)	false
N	O	HOH- 295	2.9	148.18	H-Bond (Ligand Donor)	false
NE	O	HOH- 322	3.23	134.55	H-Bond (Ligand Donor)	false