scPDB - 4dfr entry

Protein Data Bank Entry:

PDB ID : 4dfr

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1982-06-25

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_ECOLI
AC:	P0ABQ4
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.5.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	22.312
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.262	1053.000

% Hydrophobic	% Polar
41.03	58.97
According to VolSite

Ligand :

HET Code:	MTX
Formula:	C20H20N8O5
Molecular weight:	452.423 g/mol
DrugBank ID:	DB00563
Buried Surface Area:	54.42 %
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
18.4408	68.7858	42.6854

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
NA4	O	ILE- 5	2.95	153.36	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 27	2.65	165.49	H-Bond (Ligand Donor)	false
NA2	OD1	ASP- 27	2.8	174.48	H-Bond (Ligand Donor)	false
CG	CB	LEU- 28	3.81	0	Hydrophobic	false
C11	CD2	LEU- 28	3.64	0	Hydrophobic	false
CB	CB	LYS- 32	4.41	0	Hydrophobic	false
C9	CG2	THR- 46	4.3	0	Hydrophobic	false
CM	CB	SER- 49	4.05	0	Hydrophobic	false
C9	CG1	ILE- 50	4.21	0	Hydrophobic	false
CM	CG1	ILE- 50	4.04	0	Hydrophobic	false
C12	CG2	ILE- 50	4.43	0	Hydrophobic	false
C14	CG1	ILE- 50	3.59	0	Hydrophobic	false
O	NH2	ARG- 52	2.7	135.39	H-Bond (Protein Donor)	false
C16	CD2	LEU- 54	3.79	0	Hydrophobic	false
O1	NH1	ARG- 57	2.91	154.35	H-Bond (Protein Donor)	false
O1	NH2	ARG- 57	3.48	134.32	H-Bond (Protein Donor)	false
O2	NH2	ARG- 57	2.68	171.27	H-Bond (Protein Donor)	false
O1	CZ	ARG- 57	3.67	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 57	3.56	0	Ionic (Protein Cationic)	false
NA4	O	ILE- 94	2.94	131.57	H-Bond (Ligand Donor)	false
O	O	HOH- 242	2.92	124.26	H-Bond (Protein Donor)	false