scPDB - 1ly4 entry

Protein Data Bank Entry:

PDB ID : 1ly4

Resolution :2.100 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:	29.199
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)
1.556	533.250

% Hydrophobic	% Polar
81.65	18.35
According to VolSite

Ligand :

HET Code:	COQ
Formula:	C17H20N6O2
Molecular weight:	340.380 g/mol
DrugBank ID:	DB03987
Buried Surface Area:	63.19 %
Polar Surface area:	112.41 Å2

Number of
H-Bond Acceptors:	8
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
14.2426	5.83256	11.2656

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	2.74	147.97	H-Bond (Ligand Donor)	false
C6B	CD2	LEU- 25	4.42	0	Hydrophobic	false
C2'	CD2	LEU- 25	4.17	0	Hydrophobic	false
CN'	CG	LEU- 25	4.05	0	Hydrophobic	false
N1'	OE1	GLU- 32	2.81	150.07	H-Bond (Ligand Donor)	false
N2'	OE2	GLU- 32	2.91	171.99	H-Bond (Ligand Donor)	false
N2'	OE1	GLU- 32	3.19	129.49	H-Bond (Ligand Donor)	false
C31	CD1	ILE- 33	4.29	0	Hydrophobic	false
C9'	CG2	THR- 61	4.45	0	Hydrophobic	false
CN'	CG2	THR- 61	4.33	0	Hydrophobic	false
C9'	CG1	ILE- 65	3.62	0	Hydrophobic	false
C31	CG	PRO- 66	4.45	0	Hydrophobic	false
C3'	CG	PRO- 66	3.84	0	Hydrophobic	false
C4'	CB	PHE- 69	4.41	0	Hydrophobic	false
C51	CG	PHE- 69	3.68	0	Hydrophobic	false
C51	CD2	LEU- 72	4.39	0	Hydrophobic	false
C5'	CD2	LEU- 72	4.36	0	Hydrophobic	false
N4'	O	ILE- 123	3.33	149.81	H-Bond (Ligand Donor)	false
CN'	C5N	NAP- 207	4.24	0	Hydrophobic	false