scPDB - 2lf1 entry

Protein Data Bank Entry:

PDB ID : 2lf1

Resolution : Å

Experimental Method : NMR

Deposition Date : 2011-06-28

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_LACCA
AC:	P00381
Organism:	Lactobacillus casei
Reign:	Bacteria
TaxID:	1582
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.366	968.625

% Hydrophobic	% Polar
61.32	38.68
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	68.49 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-3.94981	-2.38765	-8.78342

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
C4D	CD1	ILE- 13	4.01	0	Hydrophobic	false
C3N	CD1	ILE- 13	4.27	0	Hydrophobic	false
N7N	O	ILE- 13	2.59	148.15	H-Bond (Ligand Donor)	false
O2D	N	GLY- 17	3.01	156.61	H-Bond (Protein Donor)	false
C2D	CB	HIS- 18	4.45	0	Hydrophobic	false
O1X	CZ	ARG- 43	3.47	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 43	3.61	0	Ionic (Protein Cationic)	false
O2A	N	ARG- 44	3.05	148.85	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 44	3.94	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 44	3.74	0	Ionic (Protein Cationic)	false
O1A	N	THR- 45	2.92	140.8	H-Bond (Protein Donor)	false
O1A	OG1	THR- 45	2.54	123.07	H-Bond (Protein Donor)	false
O1N	OG1	THR- 45	2.89	138.3	H-Bond (Protein Donor)	false
C5N	CG2	THR- 45	3.5	0	Hydrophobic	false
O5B	N	GLY- 99	3.38	133.05	H-Bond (Protein Donor)	false
C5D	CB	ALA- 100	4.41	0	Hydrophobic	false
C3B	CG	GLN- 101	3.5	0	Hydrophobic	false
C2B	CB	GLN- 101	4.39	0	Hydrophobic	false
C5B	CB	GLN- 101	3.55	0	Hydrophobic	false
C5B	CG1	ILE- 102	4.09	0	Hydrophobic	false
C1B	CD1	ILE- 102	4.26	0	Hydrophobic	false
C5D	CG2	THR- 126	3.62	0	Hydrophobic	false
C4D	CG2	THR- 126	3.93	0	Hydrophobic	false