scPDB - 3n76 entry

Protein Data Bank Entry:

PDB ID : 3n76

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-05-26

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
A	100 %

Ligand binding site composition:

B-Factor:	18.575
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.263	243.000

% Hydrophobic	% Polar
51.39	48.61
According to VolSite

Ligand :

HET Code:	CA2
Formula:	C16H21O6
Molecular weight:	309.334 g/mol
DrugBank ID:	DB04656
Buried Surface Area:	75.26 %
Polar Surface area:	110.05 Å2

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

Mass center Coordinates

X	Y	Z
-38.9174	-60.9041	-48.2297

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
C12	CB	ASN- 12	3.82	0	Hydrophobic	false
C15	CB	ARG- 15	3.77	0	Hydrophobic	false
C16	CD2	LEU- 16	4.2	0	Hydrophobic	false
C14	CB	ARG- 19	3.83	0	Hydrophobic	false
C15	CB	GLU- 20	4.15	0	Hydrophobic	false
C14	CG	GLU- 20	3.74	0	Hydrophobic	false
C4	CZ	TYR- 24	4.42	0	Hydrophobic	false
C10	CE1	TYR- 24	4.11	0	Hydrophobic	false
C1	CE2	TYR- 24	4.16	0	Hydrophobic	false
C16	CB	TYR- 24	4.08	0	Hydrophobic	false
O1	ND2	ASN- 75	2.77	154.82	H-Bond (Protein Donor)	false
O3	OD1	ASN- 75	2.92	162.42	H-Bond (Ligand Donor)	false
O5	NE2	HIS- 81	2.9	165.24	H-Bond (Ligand Donor)	false
C1	CB	HIS- 101	4.41	0	Hydrophobic	false
O1	N	ILE- 102	2.81	150.91	H-Bond (Protein Donor)	false
O2	OG	SER- 103	2.62	171.36	H-Bond (Protein Donor)	false
O2	N	SER- 103	2.81	151.09	H-Bond (Protein Donor)	false
C6	CG1	VAL- 105	3.71	0	Hydrophobic	false
O5	NH1	ARG- 112	2.7	154.79	H-Bond (Protein Donor)	false
O4	O	HOH- 203	3.27	154.33	H-Bond (Ligand Donor)	false