scPDB - 4htf entry

Protein Data Bank Entry:

PDB ID : 4htf

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2012-11-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA 5-carboxymethoxyuridine methyltransferase
ID:	CMOM_ECO57
AC:	Q8XDG3
Organism:	Escherichia coli O157:H7
Reign:	Bacteria
TaxID:	83334
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.792
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.337	239.625

% Hydrophobic	% Polar
60.56	39.44
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	53.28 %
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
46.5339	37.0193	23.5891

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
OXT	NH2	ARG- 26	3.02	123.01	H-Bond (Protein Donor)	false
N	O	GLY- 52	2.78	164.58	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 73	2.83	177.2	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 73	2.94	168.71	H-Bond (Ligand Donor)	false
N3	N	LEU- 74	3.44	150.06	H-Bond (Protein Donor)	false
N1	N	ALA- 102	3.03	167.58	H-Bond (Protein Donor)	false
N6	OE1	GLN- 103	3.24	168.78	H-Bond (Ligand Donor)	false
N	O	HIS- 119	3.08	162.9	H-Bond (Ligand Donor)	false
CG	CB	ALA- 120	4.06	0	Hydrophobic	false
CE	CB	ALA- 120	4.5	0	Hydrophobic	false
C5'	CG2	VAL- 121	4.37	0	Hydrophobic	false