scPDB - 1dyj entry

Protein Data Bank Entry:

PDB ID : 1dyj

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 1994-10-26

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
B	100 %

Ligand binding site composition:

B-Factor:	16.404
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.327	1245.375

% Hydrophobic	% Polar
41.46	58.54
According to VolSite

Ligand :

HET Code:	DDF
Formula:	C21H23N5O6
Molecular weight:	441.437 g/mol
DrugBank ID:	DB12769
Buried Surface Area:	54.24 %
Polar Surface area:	188.86 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
18.342	68.4635	43.9637

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
NA2	OD2	ASP- 27	3.49	131.05	H-Bond (Ligand Donor)	false
NA2	OD1	ASP- 27	2.88	169.8	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 27	2.76	171.19	H-Bond (Ligand Donor)	false
CB	CB	LEU- 28	4.24	0	Hydrophobic	false
C11	CD2	LEU- 28	4.09	0	Hydrophobic	false
C9	CE2	PHE- 31	4.04	0	Hydrophobic	false
CB	CD	LYS- 32	4.28	0	Hydrophobic	false
C13	CG1	ILE- 50	4.13	0	Hydrophobic	false
C14	CD1	ILE- 50	4.02	0	Hydrophobic	false
C16	CD2	LEU- 54	3.96	0	Hydrophobic	false
O1	NH1	ARG- 57	2.6	172.15	H-Bond (Protein Donor)	false
O1	NH2	ARG- 57	3.33	128.63	H-Bond (Protein Donor)	false
O2	NH2	ARG- 57	2.71	170.36	H-Bond (Protein Donor)	false
O1	CZ	ARG- 57	3.42	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 57	3.66	0	Ionic (Protein Cationic)	false
O4	O	HOH- 427	2.75	179.99	H-Bond (Protein Donor)	false
NA2	O	HOH- 459	2.97	135.18	H-Bond (Ligand Donor)	false