scPDB - 3dmh entry

Protein Data Bank Entry:

PDB ID : 3dmh

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2008-07-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable ribosomal RNA small subunit methyltransferase
ID:	Q5SKW0_THET8
AC:	Q5SKW0
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.510
Number of residues:	45
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	GMP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.729	715.500

% Hydrophobic	% Polar
41.98	58.02
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	69.87 %
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
28.1989	57.3373	18.328

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
SD	CD2	PHE- 207	3.37	0	Hydrophobic	false
CE	CE2	PHE- 207	3.57	0	Hydrophobic	false
C3'	CB	PHE- 207	4.44	0	Hydrophobic	false
CG	CD2	PHE- 207	3.65	0	Hydrophobic	false
O	OG	SER- 216	2.57	152.82	H-Bond (Protein Donor)	false
N	O	GLY- 241	2.8	166.61	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 262	2.68	163.84	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 262	2.57	161.58	H-Bond (Ligand Donor)	false
N3	N	ASP- 263	3.31	142.11	H-Bond (Protein Donor)	false
N6	OD1	ASP- 288	2.95	153.75	H-Bond (Ligand Donor)	false
N1	N	VAL- 289	2.87	162.19	H-Bond (Protein Donor)	false
O	ND2	ASN- 305	3.49	146.67	H-Bond (Protein Donor)	false
CG	CB	ASN- 305	3.99	0	Hydrophobic	false
C5'	CB	PRO- 307	4.34	0	Hydrophobic	false
CE	CE2	PHE- 308	4.23	0	Hydrophobic	false
N	O	HOH- 392	2.92	168.88	H-Bond (Ligand Donor)	false
N6	O	HOH- 396	3.04	130.71	H-Bond (Ligand Donor)	false
O3'	O	HOH- 400	2.74	167.78	H-Bond (Protein Donor)	false