scPDB - 1s3w entry

Protein Data Bank Entry:

PDB ID : 1s3w

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2004-01-14

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_HUMAN
AC:	P00374
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	26.809
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.265	448.875

% Hydrophobic	% Polar
71.43	28.57
According to VolSite

Ligand :

HET Code:	TQT
Formula:	C17H35N5
Molecular weight:	309.493 g/mol
DrugBank ID:	DB02559
Buried Surface Area:	70.83 %
Polar Surface area:	85.11 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	5
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
30.5773	13.9276	-1.07245

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	3.1	163.73	H-Bond (Ligand Donor)	false
N2'	O	VAL- 8	3.42	122.29	H-Bond (Ligand Donor)	false
C'4	CB	ASP- 21	4.44	0	Hydrophobic	false
C7'	CD2	LEU- 22	4.07	0	Hydrophobic	false
C'5	CD2	LEU- 22	3.92	0	Hydrophobic	false
C'3	CD1	LEU- 22	3.26	0	Hydrophobic	false
N1'	OE2	GLU- 30	2.99	161.54	H-Bond (Ligand Donor)	false
N2'	OE1	GLU- 30	2.65	176.1	H-Bond (Ligand Donor)	false
C8'	CD1	PHE- 31	3.82	0	Hydrophobic	false
C'0	CE1	PHE- 31	3.2	0	Hydrophobic	false
C6'	CE1	PHE- 31	3.83	0	Hydrophobic	false
C6'	CE2	PHE- 34	3.99	0	Hydrophobic	false
C5'	CE1	PHE- 34	3.96	0	Hydrophobic	false
C8'	CG	PHE- 34	4.3	0	Hydrophobic	false
C'3	CB	SER- 59	3.99	0	Hydrophobic	false
C9'	CG1	ILE- 60	4.41	0	Hydrophobic	false
C'1	CG1	ILE- 60	4.42	0	Hydrophobic	false
C'7	CG	PRO- 61	4.49	0	Hydrophobic	false
N4'	O	VAL- 115	3.17	127.34	H-Bond (Ligand Donor)	false
C5'	C4N	NAP- 187	3.87	0	Hydrophobic	false
C'3	C2D	NAP- 187	3.88	0	Hydrophobic	false