scPDB - 3iv6 entry

Protein Data Bank Entry:

PDB ID : 3iv6

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2009-08-31

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:	Q3IV08_RHOS4
AC:	Q3IV08
Organism:	Rhodobacter sphaeroides
Reign:	Bacteria
TaxID:	272943
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.704
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.679	1107.000

% Hydrophobic	% Polar
41.77	58.23
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	76.29 %
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
43.2664	73.9533	-27.532

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
C5'	CH2	TRP- 11	3.49	0	Hydrophobic	false
C4'	CZ3	TRP- 11	4.41	0	Hydrophobic	false
C3'	CE3	TRP- 11	3.46	0	Hydrophobic	false
C2'	CD2	TRP- 11	3.67	0	Hydrophobic	false
OXT	OG	SER- 52	3.13	162.1	H-Bond (Protein Donor)	false
O3'	N	SER- 52	3.35	129.21	H-Bond (Protein Donor)	false
C3'	CB	SER- 52	3.92	0	Hydrophobic	false
O3'	OD2	ASP- 71	2.56	167.37	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 71	2.65	143.51	H-Bond (Ligand Donor)	false
N3	N	PHE- 72	3.48	134.95	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 72	3.66	0	Aromatic Face/Face	false
C2'	CE2	PHE- 72	3.75	0	Hydrophobic	false
N6	OD1	ASP- 95	3.08	153.83	H-Bond (Ligand Donor)	false
N1	N	ILE- 96	3.44	149.9	H-Bond (Protein Donor)	false
SD	CD1	LEU- 116	4.04	0	Hydrophobic	false
CE	CB	LEU- 116	3.66	0	Hydrophobic	false
C1'	CD1	LEU- 116	4.34	0	Hydrophobic	false
SD	CG	ARG- 119	3.82	0	Hydrophobic	false