scPDB - 1yt0 entry

Protein Data Bank Entry:

PDB ID : 1yt0

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2005-02-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endoplasmin
ID:	ENPL_CANLF
AC:	P41148
Organism:	Canis lupus familiaris
Reign:	Eukaryota
TaxID:	9615
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.847
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.795	459.000

% Hydrophobic	% Polar
51.47	48.53
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	46.18 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
13.5733	32.1992	16.9254

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
N1	O	HOH- 2	2.94	154.15	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 107	2.98	128.03	H-Bond (Protein Donor)	false
N6	OD1	ASP- 149	3.05	174.16	H-Bond (Ligand Donor)	false
C1'	SD	MET- 154	3.85	0	Hydrophobic	false
C4'	CB	ASN- 162	4.16	0	Hydrophobic	false
C1'	CB	ASN- 162	4.16	0	Hydrophobic	false
C1'	CD2	LEU- 163	4.43	0	Hydrophobic	false
O1A	N	PHE- 199	2.92	169.81	H-Bond (Protein Donor)	false
O2A	N	PHE- 199	3.45	127.22	H-Bond (Protein Donor)	false
O1B	MG	MG- 338	2.42	0	Metal Acceptor	false
O2A	MG	MG- 338	2.57	0	Metal Acceptor	false