scPDB - 1df7 entry

Protein Data Bank Entry:

PDB ID : 1df7

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1999-11-17

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:	17.837
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.763	583.875

% Hydrophobic	% Polar
48.55	51.45
According to VolSite

Ligand :

HET Code:	MTX
Formula:	C20H20N8O5
Molecular weight:	452.423 g/mol
DrugBank ID:	DB00563
Buried Surface Area:	63.61 %
Polar Surface area:	216.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
3.10006	27.2117	11.5768

Binding mode :

What is Poseview ?

2D View
3D View

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
NA4	O	ILE- 5	2.82	151.13	H-Bond (Ligand Donor)	false
C9	CD1	ILE- 20	4.08	0	Hydrophobic	false
CM	CD1	ILE- 20	4.14	0	Hydrophobic	false
N1	OD2	ASP- 27	2.64	159.95	H-Bond (Ligand Donor)	false
NA2	OD1	ASP- 27	2.88	176.75	H-Bond (Ligand Donor)	false
NA2	OD2	ASP- 27	3.39	128.7	H-Bond (Ligand Donor)	false
CG	CB	GLN- 28	4.14	0	Hydrophobic	false
O2	NH1	ARG- 32	3	148.06	H-Bond (Protein Donor)	false
CB	CD	ARG- 32	3.96	0	Hydrophobic	false
C9	CD2	LEU- 50	4.16	0	Hydrophobic	false
CM	CD2	LEU- 50	4.2	0	Hydrophobic	false
C14	CD2	LEU- 50	3.71	0	Hydrophobic	false
C13	CG	PRO- 51	4.14	0	Hydrophobic	false
C12	CG2	VAL- 54	4.17	0	Hydrophobic	false
C16	CD2	LEU- 57	3.96	0	Hydrophobic	false
O1	CZ	ARG- 60	3.54	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 60	3.74	0	Ionic (Protein Cationic)	false
O1	NH1	ARG- 60	2.79	166.93	H-Bond (Protein Donor)	false
O1	NH2	ARG- 60	3.43	130.8	H-Bond (Protein Donor)	false
O2	NH2	ARG- 60	2.86	168.72	H-Bond (Protein Donor)	false
NA4	O	ILE- 94	2.92	136.05	H-Bond (Ligand Donor)	false
C9	C4N	NDP- 500	4.37	0	Hydrophobic	false
NA2	O	HOH- 508	3.02	133.3	H-Bond (Ligand Donor)	false