scPDB - 1dg5 entry

Protein Data Bank Entry:

PDB ID : 1dg5

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1999-11-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrofolate reductase
ID:	DYR_MYCTU
AC:	P9WNX1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	20.822
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.721	607.500

% Hydrophobic	% Polar
49.44	50.56
According to VolSite

Ligand :

HET Code:	TOP
Formula:	C14H18N4O3
Molecular weight:	290.318 g/mol
DrugBank ID:	DB00440
Buried Surface Area:	58.13 %
Polar Surface area:	105.51 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
5.63462	25.669	12.1723

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
N7	O	ILE- 5	2.76	161.83	H-Bond (Ligand Donor)	false
C14	CG1	ILE- 20	3.84	0	Hydrophobic	false
C11	CD1	ILE- 20	4.07	0	Hydrophobic	false
N2	OD1	ASP- 27	3.5	131.3	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 27	2.67	172.06	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 27	2.81	171.29	H-Bond (Ligand Donor)	false
C9	CE1	PHE- 31	3.86	0	Hydrophobic	false
C20	CD2	PHE- 31	3.86	0	Hydrophobic	false
C14	CB	SER- 49	3.91	0	Hydrophobic	false
C15	CD2	LEU- 50	3.66	0	Hydrophobic	false
N7	O	ILE- 94	2.85	144.19	H-Bond (Ligand Donor)	false
C9	CB	ILE- 94	4.49	0	Hydrophobic	false
C9	C4N	NDP- 200	3.5	0	Hydrophobic	false
C14	C2D	NDP- 200	3.93	0	Hydrophobic	false