scPDB - 2bh2 entry

Protein Data Bank Entry:

PDB ID : 2bh2

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2005-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
ID:	RLMD_ECOLI
AC:	P55135
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.717
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.686	1221.750

% Hydrophobic	% Polar
38.67	61.33
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	67.47 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
73.627	-7.21338	18.026

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
CB	CD2	PHE- 263	3.85	0	Hydrophobic	false
CG	CE2	PHE- 263	3.56	0	Hydrophobic	false
SD	CD2	PHE- 263	3.48	0	Hydrophobic	false
O	NE2	GLN- 265	2.97	167.71	H-Bond (Protein Donor)	false
N	O	PHE- 294	2.97	150.73	H-Bond (Ligand Donor)	false
C1'	CD1	PHE- 294	4.12	0	Hydrophobic	false
C4'	CB	PHE- 294	3.81	0	Hydrophobic	false
O	ND2	ASN- 299	2.94	137.98	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 315	3.3	122.77	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 315	2.7	175.02	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 315	2.62	164.05	H-Bond (Ligand Donor)	false
N3	N	GLY- 316	3	122.26	H-Bond (Protein Donor)	false
N6	OD1	ASN- 342	3.05	155.84	H-Bond (Ligand Donor)	false
N1	N	LEU- 343	2.77	171.84	H-Bond (Protein Donor)	false
N	OD2	ASP- 363	3.1	147.15	H-Bond (Ligand Donor)	false
N	O	HOH- 2089	3.1	165.02	H-Bond (Ligand Donor)	false
OXT	O	HOH- 2135	2.83	179.96	H-Bond (Protein Donor)	false