scPDB - 4y6u entry

Protein Data Bank Entry:

PDB ID : 4y6u

Resolution :2.270 Å

Experimental Method : X-ray

Deposition Date : 2015-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucosyl-3-phosphoglycerate synthase
ID:	GPGS_MYCTU
AC:	P9WMW9
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.4.1.266

Chains:

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

Ligand binding site composition:

B-Factor:	46.836
Number of residues:	49
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.344	718.875

% Hydrophobic	% Polar
44.60	55.40
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	74.58 %
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
36.245	-9.25792	27.3498

Binding mode :

What is Poseview ?

2D View
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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
C1C	CB	PRO- 50	4.37	0	Hydrophobic	false
O3C	O	PRO- 50	3.21	149.32	H-Bond (Ligand Donor)	false
O2C	N	LEU- 52	3	165.21	H-Bond (Protein Donor)	false
O2C	OE2	GLU- 54	2.94	166.16	H-Bond (Ligand Donor)	false
N3	OG	SER- 81	3.17	162.38	H-Bond (Ligand Donor)	false
C1C	CG	LYS- 114	4.32	0	Hydrophobic	false
C5C	CD	LYS- 114	4.21	0	Hydrophobic	false
O3'	NZ	LYS- 114	2.61	142.51	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 134	2.67	161.18	H-Bond (Ligand Donor)	false
C4C	CB	ASP- 134	4.23	0	Hydrophobic	false
O3C	N	SER- 135	3.13	167.93	H-Bond (Protein Donor)	false
C6'	CB	LEU- 209	4.3	0	Hydrophobic	false
O2A	OH	TYR- 229	2.73	133.98	H-Bond (Protein Donor)	false
C6'	CB	TYR- 229	4.02	0	Hydrophobic	false
C5'	CD1	TYR- 229	3.96	0	Hydrophobic	false
O6'	OE2	GLU- 232	2.64	156.8	H-Bond (Ligand Donor)	false
O2'	NH1	ARG- 256	3.17	149.96	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 256	3.26	145.56	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 259	3.27	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 259	3.6	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 259	2.92	127.53	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 259	2.92	127.28	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 259	2.85	149.66	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 261	3.97	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 261	3.08	155.39	H-Bond (Protein Donor)	false
C1'	SD	MET- 269	4.27	0	Hydrophobic	false
C5'	SD	MET- 269	3.66	0	Hydrophobic	false
O1A	MN	MN- 401	2.25	0	Metal Acceptor	false
O2B	MN	MN- 401	2.35	0	Metal Acceptor	false
O6'	O	HOH- 525	2.97	179.97	H-Bond (Protein Donor)	false