scPDB - 3gan entry

Protein Data Bank Entry:

PDB ID : 3gan

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-02-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protein RDM1
ID:	RDM1_ARATH
AC:	Q9LUJ3
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.529
Number of residues:	26
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.764	320.625

% Hydrophobic	% Polar
66.32	33.68
According to VolSite

Ligand :

HET Code:	SVR
Formula:	C51H34N6O23S6
Molecular weight:	1291.232 g/mol
DrugBank ID:	DB04786
Buried Surface Area:	25 %
Polar Surface area:	551 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	8
Aromatic rings:	8
Anionic atoms:	6
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
41.3781	14.5648	-1.69617

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
C14	CD	ARG- 41	4.07	0	Hydrophobic	false
C27	CD1	TYR- 45	4.38	0	Hydrophobic	false
O45	OH	TYR- 48	2.64	135.24	H-Bond (Protein Donor)	false
N53	OH	TYR- 48	3.01	161.45	H-Bond (Ligand Donor)	false
C70	CB	GLN- 51	4.03	0	Hydrophobic	false
C56	CG2	VAL- 52	4.38	0	Hydrophobic	false
C68	CG	PRO- 53	3.44	0	Hydrophobic	false
C47	CB	PRO- 81	4.31	0	Hydrophobic	false
C49	CG	PRO- 81	4.43	0	Hydrophobic	false
C48	CB	PRO- 81	3.87	0	Hydrophobic	false
C27	CH2	TRP- 140	3.66	0	Hydrophobic	false
C27	CD1	ILE- 150	3.36	0	Hydrophobic	false
C37	CG2	ILE- 150	3.91	0	Hydrophobic	false
N41	O	ASP- 151	2.95	129.94	H-Bond (Ligand Donor)	false
C48	CB	ASP- 151	4.46	0	Hydrophobic	false
N44	O	PRO- 152	2.84	177.25	H-Bond (Ligand Donor)	false
C37	CG1	ILE- 153	3.67	0	Hydrophobic	false
C42	CG1	ILE- 153	3.86	0	Hydrophobic	false
C48	CG	PRO- 155	3.75	0	Hydrophobic	false