scPDB - 2jd1 entry

Protein Data Bank Entry:

PDB ID : 2jd1

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-01-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1-deoxy-D-xylulose 5-phosphate reductoisomerase
ID:	DXR_MYCTU
AC:	P9WNS1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.410
Number of residues:	54
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
1.273	705.375

% Hydrophobic	% Polar
55.50	44.50
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	62.6 %
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
12.8322	6.77171	-8.29623

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	OG1	THR- 21	2.67	168.97	H-Bond (Ligand Donor)	false
O3B	N	THR- 21	3.23	122.6	H-Bond (Protein Donor)	false
O2X	OG1	THR- 21	2.64	153.38	H-Bond (Protein Donor)	false
O2A	N	SER- 23	3.15	174	H-Bond (Protein Donor)	false
O2N	N	ILE- 24	3.05	178.44	H-Bond (Protein Donor)	false
C4N	CD1	ILE- 24	4.39	0	Hydrophobic	false
O2B	N	GLY- 47	3.07	172.37	H-Bond (Protein Donor)	false
O3X	N	ALA- 49	3.03	168.93	H-Bond (Protein Donor)	false
O2X	N	HIS- 50	3.28	126.02	H-Bond (Protein Donor)	false
C1B	CD2	LEU- 104	4.26	0	Hydrophobic	false
C5B	CB	VAL- 105	4.12	0	Hydrophobic	false
C3D	CG2	VAL- 105	4.16	0	Hydrophobic	false
C4D	CB	ALA- 126	4.24	0	Hydrophobic	false
C1D	CB	ALA- 126	4.16	0	Hydrophobic	false
O3D	OE2	GLU- 129	3.47	150.04	H-Bond (Ligand Donor)	false
O1N	N	GLY- 206	3.31	157.47	H-Bond (Protein Donor)	false
O2D	OD1	ASN- 209	3.12	152.79	H-Bond (Ligand Donor)	false
C4N	CE	MET- 267	3.95	0	Hydrophobic	false
O7N	O	HOH- 2119	2.88	154.82	H-Bond (Protein Donor)	false