scPDB - 3zhx entry

Protein Data Bank Entry:

PDB ID : 3zhx

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.680	6.680	6.680	0.000	6.680	1

List of CHEMBLId :

CHEMBL2407184

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:	19.283
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.358	641.250

% Hydrophobic	% Polar
35.26	64.74
According to VolSite

Ligand :

HET Code:	FM6
Formula:	C16H14Cl2NO5P
Molecular weight:	402.166 g/mol
DrugBank ID:	-
Buried Surface Area:	47.29 %
Polar Surface area:	113.54 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
20.3425	21.9865	-17.3824

Binding mode :

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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
O1	OG	SER- 152	2.93	155.87	H-Bond (Protein Donor)	false
C13	CB	SER- 152	4.09	0	Hydrophobic	false
OP3	N	SER- 177	2.81	165.82	H-Bond (Protein Donor)	false
OP2	OG	SER- 177	2.78	170.7	H-Bond (Protein Donor)	false
C7	CB	SER- 177	4.09	0	Hydrophobic	false
OP2	OG	SER- 213	2.55	157.31	H-Bond (Protein Donor)	false
C3	CB	SER- 213	4.04	0	Hydrophobic	false
OP1	ND2	ASN- 218	2.74	159.02	H-Bond (Protein Donor)	false
O2	ND2	ASN- 218	2.94	136.57	H-Bond (Protein Donor)	false
OP1	NZ	LYS- 219	3.04	120.32	H-Bond (Protein Donor)	false
OP3	NZ	LYS- 219	2.87	145.91	H-Bond (Protein Donor)	false
OP1	NZ	LYS- 219	3.04	0	Ionic (Protein Cationic)	false
OP3	NZ	LYS- 219	2.87	0	Ionic (Protein Cationic)	false
CL2	CB	SER- 245	3.48	0	Hydrophobic	false
CL2	CB	PRO- 265	3.7	0	Hydrophobic	false
C15	CG	MET- 267	3.83	0	Hydrophobic	false
C13	SD	MET- 267	3.82	0	Hydrophobic	false
O2	MN	MN- 401	2.15	0	Metal Acceptor	false
O1	MN	MN- 401	2.19	0	Metal Acceptor	false
OP2	O	HOH- 2088	2.99	169.73	H-Bond (Protein Donor)	false