scPDB - 2y88 entry

Protein Data Bank Entry:

PDB ID : 2y88

Resolution :1.330 Å

Experimental Method : X-ray

Deposition Date : 2011-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoribosyl isomerase A
ID:	HIS4_MYCTU
AC:	P9WMM5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	5.3.1.16

Chains:

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

Ligand binding site composition:

B-Factor:	16.156
Number of residues:	62
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	8
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.066	425.250

% Hydrophobic	% Polar
36.51	63.49
According to VolSite

Ligand :

HET Code:	2ER
Formula:	C15H22N5O15P2
Molecular weight:	574.307 g/mol
DrugBank ID:	-
Buried Surface Area:	76.3 %
Polar Surface area:	358.59 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	7
Rings:	2
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
40.497	9.21992	1.75165

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
C3''	CB	ALA- 9	4.2	0	Hydrophobic	false
O2B	ND2	ASN- 11	2.64	157.1	H-Bond (Protein Donor)	false
O8B	NH2	ARG- 19	2.92	136.24	H-Bond (Protein Donor)	false
O8B	NE	ARG- 19	2.71	156.22	H-Bond (Protein Donor)	false
O8B	CZ	ARG- 19	3.23	0	Ionic (Protein Cationic)	false
N9	O	GLY- 23	3.12	168.22	H-Bond (Ligand Donor)	false
C1'	CG1	VAL- 52	3.98	0	Hydrophobic	false
C4'	CG1	VAL- 52	4.37	0	Hydrophobic	false
C4'	CB	ALA- 57	4.47	0	Hydrophobic	false
O3'	OG	SER- 81	2.83	162.11	H-Bond (Protein Donor)	false
C4'	CB	SER- 81	3.89	0	Hydrophobic	false
O8'	N	GLY- 83	2.6	151.91	H-Bond (Protein Donor)	false
O8'	NE	ARG- 85	2.9	143.01	H-Bond (Protein Donor)	false
O8'	NH2	ARG- 85	2.81	147.83	H-Bond (Protein Donor)	false
O8'	CZ	ARG- 85	3.29	0	Ionic (Protein Cationic)	false
O'1	N	GLY- 104	2.96	149.06	H-Bond (Protein Donor)	false
O9'	OG1	THR- 105	2.61	157.43	H-Bond (Protein Donor)	false
O9'	N	THR- 105	2.81	159.18	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 130	2.57	148.51	H-Bond (Ligand Donor)	false
N9	O	GLY- 144	2.97	143.23	H-Bond (Ligand Donor)	false
O4B	OD1	ASP- 175	2.59	151.02	H-Bond (Ligand Donor)	false
N8	OD1	ASP- 175	3.96	0	Ionic (Ligand Cationic)	false
N8	OD2	ASP- 175	3.12	0	Ionic (Ligand Cationic)	false
O'L	N	GLY- 176	2.75	164.83	H-Bond (Protein Donor)	false
O4B	OG	SER- 200	2.55	145.99	H-Bond (Protein Donor)	false
O'L	N	GLY- 202	2.83	165.34	H-Bond (Protein Donor)	false
C4B	CG2	ILE- 224	3.57	0	Hydrophobic	false
O9B	N	GLY- 226	2.78	160.3	H-Bond (Protein Donor)	false
O8B	N	LYS- 227	2.72	170.17	H-Bond (Protein Donor)	false
O'1	O	HOH- 2390	2.64	166.38	H-Bond (Protein Donor)	false
O9B	O	HOH- 2391	2.6	179.94	H-Bond (Protein Donor)	false
O'1	O	HOH- 2392	2.6	179.97	H-Bond (Protein Donor)	false
O'L	O	HOH- 2393	2.78	179.96	H-Bond (Protein Donor)	false
O9B	O	HOH- 2394	2.66	179.96	H-Bond (Protein Donor)	false