scPDB - 3b4y entry

Protein Data Bank Entry:

PDB ID : 3b4y

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2007-10-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	F420-dependent glucose-6-phosphate dehydrogenase
ID:	FGD_MYCTU
AC:	P9WNE1
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:	18.494
Number of residues:	47
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.458	661.500

% Hydrophobic	% Polar
38.27	61.73
According to VolSite

Ligand :

HET Code:	F42
Formula:	C29H32N5O18P
Molecular weight:	769.561 g/mol
DrugBank ID:	DB03913
Buried Surface Area:	59.53 %
Polar Surface area:	389.68 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-11.0759	16.2913	38.8242

Binding mode :

What is Poseview ?

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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
N3	O	ASP- 39	2.78	171.07	H-Bond (Ligand Donor)	false
O4	N	ASP- 39	2.91	148.01	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 74	4.39	0	Hydrophobic	false
C5A	CG2	VAL- 74	3.81	0	Hydrophobic	false
C9A	CG2	VAL- 74	3.63	0	Hydrophobic	false
O2P	OG1	THR- 107	2.56	137.69	H-Bond (Protein Donor)	false
O2'	N	GLY- 108	3.21	147.97	H-Bond (Protein Donor)	false
O2	ND2	ASN- 112	3.21	128.5	H-Bond (Protein Donor)	false
C1I	CD1	PHE- 125	3.87	0	Hydrophobic	false
C3H	CE2	PHE- 125	4.21	0	Hydrophobic	false
C4H	CD2	PHE- 125	3.77	0	Hydrophobic	false
C8	CB	ALA- 175	3.81	0	Hydrophobic	false
O1P	N	GLY- 177	2.71	160.73	H-Bond (Protein Donor)	false
O1P	N	GLY- 178	3.3	135.4	H-Bond (Protein Donor)	false
O2U	N	ALA- 180	3.11	165.87	H-Bond (Protein Donor)	false
O2T	N	VAL- 181	3.32	153.14	H-Bond (Protein Donor)	false
C7	CG2	ILE- 193	3.82	0	Hydrophobic	false
C7	CG2	THR- 195	3.53	0	Hydrophobic	false
O2	O	HOH- 341	2.67	179.97	H-Bond (Protein Donor)	false
O3'	O	HOH- 352	3.32	128.06	H-Bond (Protein Donor)	false