scPDB - 2dqs entry

Protein Data Bank Entry:

PDB ID : 2dqs

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2006-05-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.700	9.700	9.700	0.000	9.700	2

List of CHEMBLId :

CHEMBL96926

Binding Site :

Uniprot Annotation

Name:	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
ID:	AT2A1_RABIT
AC:	P04191
Organism:	Oryctolagus cuniculus
Reign:	Eukaryota
TaxID:	9986
EC Number:	3.6.3.8

Chains:

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

Ligand binding site composition:

B-Factor:	66.732
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.892	1765.125

% Hydrophobic	% Polar
61.57	38.43
According to VolSite

Ligand :

HET Code:	TG1
Formula:	C34H50O12
Molecular weight:	650.754 g/mol
DrugBank ID:	-
Buried Surface Area:	59.04 %
Polar Surface area:	171.95 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	2
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
31.0044	-23.7297	83.7373

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
C30	CD1	LEU- 253	3.75	0	Hydrophobic	false
C25	CZ	PHE- 256	3.78	0	Hydrophobic	false
C26	CE1	PHE- 256	4.11	0	Hydrophobic	false
C6	CD1	PHE- 256	4.02	0	Hydrophobic	false
C31	CE1	PHE- 256	3.99	0	Hydrophobic	false
C28	CD1	PHE- 256	4.23	0	Hydrophobic	false
C29	CB	PHE- 256	3.89	0	Hydrophobic	false
C26	CB	GLN- 259	3.59	0	Hydrophobic	false
C25	CD1	LEU- 260	3.56	0	Hydrophobic	false
C26	CB	LEU- 260	4.19	0	Hydrophobic	false
C17	CG1	VAL- 263	4.41	0	Hydrophobic	false
C3	CG2	VAL- 263	4.32	0	Hydrophobic	false
C26	CG2	VAL- 263	4.03	0	Hydrophobic	false
C19	CD1	ILE- 267	3.61	0	Hydrophobic	false
C30	CG2	ILE- 761	4.47	0	Hydrophobic	false
C25	CG2	ILE- 765	4.17	0	Hydrophobic	false
C31	CG2	ILE- 765	3.4	0	Hydrophobic	false
C30	CD1	ILE- 765	3.55	0	Hydrophobic	false
C25	CB	ASN- 768	3.82	0	Hydrophobic	false
C23	CG2	VAL- 769	4.04	0	Hydrophobic	false
C25	CG2	VAL- 769	4.29	0	Hydrophobic	false
C31	CG2	VAL- 769	4.27	0	Hydrophobic	false
C33	CG2	VAL- 769	3.89	0	Hydrophobic	false
C23	CB	VAL- 772	3.68	0	Hydrophobic	false
C20	CD2	PHE- 776	4.11	0	Hydrophobic	false
C29	CD1	LEU- 828	4	0	Hydrophobic	false
C8	CB	ILE- 829	3.9	0	Hydrophobic	false
C9	CG2	ILE- 829	3.59	0	Hydrophobic	false
C28	CD1	ILE- 829	4.09	0	Hydrophobic	false
O8	N	ILE- 829	3.1	121.52	H-Bond (Protein Donor)	false
C9	CD2	PHE- 834	4.21	0	Hydrophobic	false
C1	CE2	PHE- 834	4.18	0	Hydrophobic	false
C14	CZ	PHE- 834	3.85	0	Hydrophobic	false
C33	CG	TYR- 837	4.25	0	Hydrophobic	false