scPDB - 1s3u entry

Protein Data Bank Entry:

PDB ID : 1s3u

Resolution :2.500 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:	13.627
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.159	756.000

% Hydrophobic	% Polar
53.57	46.43
According to VolSite

Ligand :

HET Code:	TQD
Formula:	C19H30N5O3
Molecular weight:	376.473 g/mol
DrugBank ID:	DB08642
Buried Surface Area:	57.69 %
Polar Surface area:	108.97 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
31.3179	15.2379	-1.08789

Binding mode :

What is Poseview ?

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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
N4'	O	ILE- 7	3.13	151.6	H-Bond (Ligand Donor)	false
N2'	O	VAL- 8	3.48	120.5	H-Bond (Ligand Donor)	false
C9'	CD2	LEU- 22	3.89	0	Hydrophobic	false
N1'	OE2	GLU- 30	2.65	152.44	H-Bond (Ligand Donor)	false
N2'	OE1	GLU- 30	2.7	135.05	H-Bond (Ligand Donor)	false
N2'	OE2	GLU- 30	3.44	125.07	H-Bond (Ligand Donor)	false
C3B	CZ	PHE- 31	4.12	0	Hydrophobic	false
C4B	CE2	PHE- 31	3.95	0	Hydrophobic	false
C7'	CE1	PHE- 31	2.88	0	Hydrophobic	false
C4A	CB	PHE- 34	4.46	0	Hydrophobic	false
C8	CB	PHE- 34	4.13	0	Hydrophobic	false
C5B	CE2	PHE- 34	4.43	0	Hydrophobic	false
C4A	CD1	PHE- 34	3.35	0	Hydrophobic	false
C8'	CG1	ILE- 60	3.92	0	Hydrophobic	false
C5'	CG2	ILE- 60	4.09	0	Hydrophobic	false
C5B	CG2	ILE- 60	4.14	0	Hydrophobic	false
C6'	CG1	ILE- 60	3.97	0	Hydrophobic	false
C3B	CG	PRO- 61	4.14	0	Hydrophobic	false
C3'	CG	PRO- 61	4.04	0	Hydrophobic	false
C5B	CB	ASN- 64	4.01	0	Hydrophobic	false
C5B	CD2	LEU- 67	3.54	0	Hydrophobic	false
N4'	O	VAL- 115	3.37	139.98	H-Bond (Ligand Donor)	false