scPDB - 3fr8 entry

Protein Data Bank Entry:

PDB ID : 3fr8

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2009-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ketol-acid reductoisomerase, chloroplastic
ID:	ILV5_ORYSJ
AC:	Q65XK0
Organism:	Oryza sativa subsp. japonica
Reign:	Eukaryota
TaxID:	39947
EC Number:	1.1.1.86

Chains:

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

Ligand binding site composition:

B-Factor:	52.677
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.463	472.500

% Hydrophobic	% Polar
39.29	60.71
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	57.05 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
22.049	31.5819	61.9253

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
O3B	N	TRP- 133	2.96	146.11	H-Bond (Protein Donor)	false
O1N	N	GLN- 136	2.84	158.93	H-Bond (Protein Donor)	false
C5D	CB	GLN- 136	4.34	0	Hydrophobic	false
C3N	CG	GLN- 136	3.84	0	Hydrophobic	false
N3A	NH1	ARG- 162	3.49	149.9	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 162	3.47	0	Ionic (Protein Cationic)	false
O2X	OG	SER- 165	3.07	151.86	H-Bond (Protein Donor)	false
O3X	OG	SER- 165	2.82	128.51	H-Bond (Protein Donor)	false
O3X	OG	SER- 167	2.84	167.04	H-Bond (Protein Donor)	false
C5D	CB	LEU- 199	4.39	0	Hydrophobic	false
C1B	CG2	ILE- 200	3.96	0	Hydrophobic	false
C5B	CB	SER- 201	4.35	0	Hydrophobic	false
O4B	N	SER- 201	3.38	139.67	H-Bond (Protein Donor)	false
O3D	OD1	ASP- 202	2.58	151.12	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 202	3.22	161	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 202	2.87	137.8	H-Bond (Ligand Donor)	false
C2D	CB	HIS- 226	3.88	0	Hydrophobic	false
C2D	CB	SER- 518	4.5	0	Hydrophobic	false
C3N	CB	SER- 518	4.07	0	Hydrophobic	false
O3D	O	HOH- 620	3.16	171.85	H-Bond (Protein Donor)	false