scPDB - 4m2a entry

Protein Data Bank Entry:

PDB ID : 4m2a

Resolution :1.660 Å

Experimental Method : X-ray

Deposition Date : 2013-08-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-glucose pyrophosphorylase
ID:	Q4QDU3_LEIMA
AC:	Q4QDU3
Organism:	Leishmania major
Reign:	Eukaryota
TaxID:	5664
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.028
Number of residues:	51
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.041	1387.125

% Hydrophobic	% Polar
37.71	62.29
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	70.73 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
22.1827	37.6131	42.0438

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
C1C	CB	LEU- 81	3.87	0	Hydrophobic	false
C3C	CB	LEU- 81	4.41	0	Hydrophobic	false
C4C	CD1	LEU- 81	3.87	0	Hydrophobic	false
O2	N	GLY- 83	2.67	132.19	H-Bond (Protein Donor)	false
O2C	N	GLY- 84	2.91	143.63	H-Bond (Protein Donor)	false
N3	OE1	GLN- 162	2.74	170.9	H-Bond (Ligand Donor)	false
C1C	CB	HIS- 191	4.44	0	Hydrophobic	false
O1B	NE2	HIS- 191	2.71	150.4	H-Bond (Protein Donor)	false
C5C	CB	ASN- 219	4.32	0	Hydrophobic	false
C4C	CB	ASN- 219	4.11	0	Hydrophobic	false
O5'	ND2	ASN- 219	3.11	150.95	H-Bond (Protein Donor)	false
O3C	N	GLY- 220	3.1	140.35	H-Bond (Protein Donor)	false
O4'	N	GLY- 257	3	154.37	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 284	3.44	120.79	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 284	2.68	164.99	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 284	2.58	176.34	H-Bond (Ligand Donor)	false
C6'	CE2	PHE- 305	4.42	0	Hydrophobic	false
O3'	ND2	ASN- 306	2.82	155	H-Bond (Protein Donor)	false
O4'	O	ASN- 306	2.59	150.05	H-Bond (Ligand Donor)	false
C4'	CB	ASN- 306	4.1	0	Hydrophobic	false
C2'	CB	ASN- 308	4.24	0	Hydrophobic	false
C6'	CB	ASN- 308	4.37	0	Hydrophobic	false
C6'	CE1	PHE- 376	3.61	0	Hydrophobic	false
O1A	NZ	LYS- 380	2.75	167.38	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 380	2.75	0	Ionic (Protein Cationic)	false
O2'	O	HOH- 2007	2.79	167.44	H-Bond (Protein Donor)	false
O6'	O	HOH- 2064	2.96	157.26	H-Bond (Ligand Donor)	false
O1A	O	HOH- 2548	2.81	179.97	H-Bond (Protein Donor)	false