scPDB - 2fzi entry

Protein Data Bank Entry:

PDB ID : 2fzi

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2006-02-09

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:	21.263
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.596	604.125

% Hydrophobic	% Polar
71.51	28.49
According to VolSite

Ligand :

HET Code:	DH3
Formula:	C19H21N4O4
Molecular weight:	369.394 g/mol
DrugBank ID:	-
Buried Surface Area:	64.13 %
Polar Surface area:	136.41 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
50.4561	1.70644	10.6934

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- 10	2.86	154.61	H-Bond (Ligand Donor)	false
C5'	CD1	LEU- 25	4.17	0	Hydrophobic	false
C3'	CD1	LEU- 25	3.72	0	Hydrophobic	false
N2	OE2	GLU- 32	2.68	163.34	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 32	3.49	124.9	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 32	2.67	175.5	H-Bond (Ligand Donor)	false
C54	CG2	ILE- 33	3.79	0	Hydrophobic	false
C7	CG2	ILE- 33	4.2	0	Hydrophobic	false
C4'	CD1	ILE- 33	4.47	0	Hydrophobic	false
C53	CD1	ILE- 33	3.68	0	Hydrophobic	false
C51	CZ	PHE- 36	3.92	0	Hydrophobic	false
C4B	CG1	ILE- 65	4.45	0	Hydrophobic	false
C7	CD2	LEU- 72	4.3	0	Hydrophobic	false
O10	CZ	ARG- 75	3.76	0	Ionic (Protein Cationic)	false
O9	CZ	ARG- 75	3.42	0	Ionic (Protein Cationic)	false
O10	NH2	ARG- 75	2.8	155.76	H-Bond (Protein Donor)	false
O9	NH1	ARG- 75	2.8	158.3	H-Bond (Protein Donor)	false
O9	NH2	ARG- 75	3.19	135.4	H-Bond (Protein Donor)	false
C51	C4N	NDP- 207	3.67	0	Hydrophobic	false
O10	O	HOH- 237	2.86	179.96	H-Bond (Protein Donor)	false