scPDB - 3k45 entry

Protein Data Bank Entry:

PDB ID : 3k45

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2009-10-05

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_MOUSE
AC:	P00375
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	28.384
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.972	499.500

% Hydrophobic	% Polar
63.51	36.49
According to VolSite

Ligand :

HET Code:	51P
Formula:	C16H16N4O2
Molecular weight:	296.324 g/mol
DrugBank ID:	-
Buried Surface Area:	65.61 %
Polar Surface area:	100.19 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-3.79533	2.03333	13.6527

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
N4'	O	ILE- 7	3.02	164.23	H-Bond (Ligand Donor)	false
N2'	O	VAL- 8	3.26	132.37	H-Bond (Ligand Donor)	false
N1'	OE2	GLU- 30	2.79	168.42	H-Bond (Ligand Donor)	false
N2'	OE1	GLU- 30	2.75	174.07	H-Bond (Ligand Donor)	false
C5'	CB	PHE- 34	4.38	0	Hydrophobic	false
C5'	CD1	PHE- 34	3.38	0	Hydrophobic	false
C10	CG2	THR- 56	3.39	0	Hydrophobic	false
C10	CD1	ILE- 60	4.02	0	Hydrophobic	false
C'5	CG2	ILE- 60	4.18	0	Hydrophobic	false
C'1	CG1	ILE- 60	4.13	0	Hydrophobic	false
C'6	CD2	LEU- 67	4.07	0	Hydrophobic	false
C10	CG2	VAL- 115	4.11	0	Hydrophobic	false
N4'	O	VAL- 115	2.96	132.4	H-Bond (Ligand Donor)	false
C10	C5N	NDP- 187	4.36	0	Hydrophobic	false