scPDB - 1yp4 entry

Protein Data Bank Entry:

PDB ID : 1yp4

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2005-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic
ID:	GLGS_SOLTU
AC:	P23509
Organism:	Solanum tuberosum
Reign:	Eukaryota
TaxID:	4113
EC Number:	2.7.7.27

Chains:

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

Ligand binding site composition:

B-Factor:	51.441
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.121	708.750

% Hydrophobic	% Polar
37.62	62.38
According to VolSite

Ligand :

HET Code:	ADQ
Formula:	C16H23N5O15P2
Molecular weight:	587.326 g/mol
DrugBank ID:	DB01774
Buried Surface Area:	66.73 %
Polar Surface area:	337.03 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	7
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
8.09024	26.6897	53.7972

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
C5D	CD2	LEU- 26	4.21	0	Hydrophobic	false
C4D	CB	LEU- 26	4.27	0	Hydrophobic	false
C1D	CB	LEU- 26	3.93	0	Hydrophobic	false
O2D	O	GLY- 27	3.3	174.81	H-Bond (Ligand Donor)	false
O1B	NH2	ARG- 33	3.41	133.94	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 33	3.3	137.29	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 33	3.76	0	Ionic (Protein Cationic)	false
O2D	NZ	LYS- 43	2.86	167.43	H-Bond (Protein Donor)	false
N6	OE1	GLN- 118	3.37	161.44	H-Bond (Ligand Donor)	false
N6	O	GLN- 118	2.65	147.74	H-Bond (Ligand Donor)	false
C5D	CG2	THR- 120	3.24	0	Hydrophobic	false
C4D	CB	ALA- 143	4.15	0	Hydrophobic	false
O3D	OD1	ASP- 145	2.91	143.59	H-Bond (Ligand Donor)	false
C6'	CD2	PHE- 181	3.49	0	Hydrophobic	false
C5'	CD2	PHE- 181	4.15	0	Hydrophobic	false
O4'	N	GLY- 182	2.97	172.63	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 197	2.83	163.62	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 197	2.82	162.7	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 198	2.51	154.84	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 198	2.51	0	Ionic (Protein Cationic)	false
C4'	CB	SER- 229	4.02	0	Hydrophobic	false
O4'	O	SER- 229	2.75	167.38	H-Bond (Ligand Donor)	false
C6'	CH2	TRP- 278	3.81	0	Hydrophobic	false