scPDB - 3n87 entry

Protein Data Bank Entry:

PDB ID : 3n87

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-dehydroquinate dehydratase
ID:	AROQ_MYCTU
AC:	P9WPX7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	4.2.1.10

Chains:

Chain Name:	Percentage of Residues within binding site
I	20 %
J	80 %

Ligand binding site composition:

B-Factor:	33.476
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.442	556.875

% Hydrophobic	% Polar
43.03	56.97
According to VolSite

Ligand :

HET Code:	N87
Formula:	C20H17O6
Molecular weight:	353.345 g/mol
DrugBank ID:	-
Buried Surface Area:	75.37 %
Polar Surface area:	117.89 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
47.1569	37.1813	11.9005

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
C24	CB	ASN- 12	3.31	0	Hydrophobic	false
C24	CG	LEU- 13	3.9	0	Hydrophobic	false
C25	CD2	LEU- 13	3.62	0	Hydrophobic	false
C20	CB	GLU- 20	3.96	0	Hydrophobic	false
C21	CB	PRO- 21	4.49	0	Hydrophobic	false
C4	CE2	TYR- 24	4.35	0	Hydrophobic	false
C14	CZ	TYR- 24	3.34	0	Hydrophobic	false
O3	ND2	ASN- 75	2.87	151.01	H-Bond (Protein Donor)	false
O5	OD1	ASN- 75	2.63	139.71	H-Bond (Ligand Donor)	false
O11	NE2	HIS- 81	2.9	172.24	H-Bond (Protein Donor)	false
C15	CB	ASP- 88	4.15	0	Hydrophobic	false
C18	CB	ALA- 91	4.5	0	Hydrophobic	false
C18	CG	GLU- 92	3.82	0	Hydrophobic	false
C19	CB	GLU- 92	3.83	0	Hydrophobic	false
C20	CG	GLU- 92	3.36	0	Hydrophobic	false
C4	CB	HIS- 101	4.45	0	Hydrophobic	false
O3	N	ILE- 102	2.51	172.3	H-Bond (Protein Donor)	false
O1	N	SER- 103	2.9	152.59	H-Bond (Protein Donor)	false
O1	OG	SER- 103	2.72	162.65	H-Bond (Protein Donor)	false
C12	CG1	VAL- 105	4.02	0	Hydrophobic	false
O11	NH1	ARG- 112	2.75	136.99	H-Bond (Protein Donor)	false