scPDB - 1ly3 entry

Protein Data Bank Entry:

PDB ID : 1ly3

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2002-06-06

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_PNECA
AC:	P16184
Organism:	Pneumocystis carinii
Reign:	Eukaryota
TaxID:	4754
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	21.209
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.367	523.125

% Hydrophobic	% Polar
73.55	26.45
According to VolSite

Ligand :

HET Code:	COG
Formula:	C18H21N5O2
Molecular weight:	339.392 g/mol
DrugBank ID:	DB02427
Buried Surface Area:	64.21 %
Polar Surface area:	99.52 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
14.2417	5.84284	11.6611

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- 10	2.95	162.37	H-Bond (Ligand Donor)	false
N2'	O	VAL- 11	3.46	122.06	H-Bond (Ligand Donor)	false
C21	CG	LEU- 25	4.16	0	Hydrophobic	false
C2'	CD1	LEU- 25	4.01	0	Hydrophobic	false
C7B	CD1	LEU- 25	3.46	0	Hydrophobic	false
N1'	OE1	GLU- 32	2.8	174.1	H-Bond (Ligand Donor)	false
N2'	OE2	GLU- 32	2.71	176.15	H-Bond (Ligand Donor)	false
C7B	CD1	ILE- 33	3.2	0	Hydrophobic	false
C5'	CD1	ILE- 33	4.07	0	Hydrophobic	false
C61	CZ	PHE- 36	4.16	0	Hydrophobic	false
C61	CG2	THR- 61	3.89	0	Hydrophobic	false
C21	CB	SER- 64	4.26	0	Hydrophobic	false
C61	CG1	ILE- 65	4.32	0	Hydrophobic	false
C5'	CG2	ILE- 65	4.39	0	Hydrophobic	false
C6'	CG1	ILE- 65	4.17	0	Hydrophobic	false
C4'	CG	PRO- 66	4.25	0	Hydrophobic	false
C51	CB	PHE- 69	3.23	0	Hydrophobic	false
C61	CD1	ILE- 123	4.17	0	Hydrophobic	false
N4'	O	ILE- 123	2.72	133.14	H-Bond (Ligand Donor)	false
N2'	O	HOH- 215	3.45	130.56	H-Bond (Ligand Donor)	false