scPDB - 3tm4 entry

Protein Data Bank Entry:

PDB ID : 3tm4

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2011-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q8U248_PYRFU
AC:	Q8U248
Organism:	Pyrococcus furiosus
Reign:	Archaea
TaxID:	186497
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.637
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.781	590.625

% Hydrophobic	% Polar
53.14	46.86
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	75.44 %
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
79.9631	30.1598	99.1344

Binding mode :

What is Poseview ?

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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
O3'	NE2	HIS- 198	3.04	155.33	H-Bond (Protein Donor)	false
CE	CB	ALA- 200	3.84	0	Hydrophobic	false
OXT	N	LEU- 202	2.94	174.49	H-Bond (Protein Donor)	false
C4'	CB	MET- 225	4.21	0	Hydrophobic	false
C1'	CB	MET- 225	4.19	0	Hydrophobic	false
O	OG	SER- 228	2.5	159.67	H-Bond (Protein Donor)	false
O	N	SER- 228	2.85	140.1	H-Bond (Protein Donor)	false
OXT	OG1	THR- 230	2.58	160.57	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 248	2.56	141.69	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 248	2.67	158.57	H-Bond (Ligand Donor)	false
N3	N	LYS- 249	3.43	130	H-Bond (Protein Donor)	false
N6	OD1	ASP- 276	2.96	158.94	H-Bond (Ligand Donor)	false
N1	N	ALA- 277	2.81	173.07	H-Bond (Protein Donor)	false
N	OD1	ASN- 293	3.29	162.35	H-Bond (Ligand Donor)	false
C5'	CG	PRO- 295	4.29	0	Hydrophobic	false
N	O	HOH- 502	3.11	173.76	H-Bond (Ligand Donor)	false