scPDB - 4rtb entry

Protein Data Bank Entry:

PDB ID : 4rtb

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2014-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative thiazole biosynthesis protein ThiH
ID:	Q3ABV3_CARHZ
AC:	Q3ABV3
Organism:	Carboxydothermus hydrogenoformans
Reign:	Bacteria
TaxID:	246194
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	83.278
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.319	448.875

% Hydrophobic	% Polar
63.91	36.09
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	69.38 %
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
46.0172	3.61456	19.3183

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
CE	CE2	TYR- 83	4.48	0	Hydrophobic	false
N6	O	TYR- 94	2.9	128.07	H-Bond (Ligand Donor)	false
CE	CD2	PHE- 97	4.37	0	Hydrophobic	false
CE	CG2	VAL- 132	3.66	0	Hydrophobic	false
C5'	CG2	VAL- 132	4.26	0	Hydrophobic	false
CG	CG2	VAL- 132	3.63	0	Hydrophobic	false
N	O	MET- 133	2.95	164.89	H-Bond (Ligand Donor)	false
CA	CB	ALA- 166	4.46	0	Hydrophobic	false
C3'	CD2	PHE- 187	4.1	0	Hydrophobic	false
O3'	OE2	GLU- 189	2.51	160.44	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 189	2.98	155.41	H-Bond (Ligand Donor)	false
O	NZ	LYS- 205	3.31	132.54	H-Bond (Protein Donor)	false
O	NZ	LYS- 205	3.31	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 211	3.31	123.16	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 211	3.34	126.86	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 211	2.59	170.64	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 211	3.39	0	Ionic (Protein Cationic)	false
C2'	CD2	LEU- 231	4.35	0	Hydrophobic	false
N6	O	LYS- 268	3.44	156.73	H-Bond (Ligand Donor)	false
N1	N	LYS- 268	3.01	169.86	H-Bond (Protein Donor)	false
O4'	NE2	GLN- 346	3.49	129.42	H-Bond (Protein Donor)	false