scPDB - 3nxv entry

Protein Data Bank Entry:

PDB ID : 3nxv

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-07-14

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:	14.193
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.144	556.875

% Hydrophobic	% Polar
61.82	38.18
According to VolSite

Ligand :

HET Code:	D2F
Formula:	C19H22N4O2
Molecular weight:	338.404 g/mol
DrugBank ID:	-
Buried Surface Area:	65.89 %
Polar Surface area:	100.19 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-3.42372	16.306	0.01628

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
CAB	CD1	LEU- 22	3.67	0	Hydrophobic	false
CAH	CG	LEU- 22	3.98	0	Hydrophobic	false
CAV	CD1	LEU- 22	3.85	0	Hydrophobic	false
CAW	CD2	LEU- 22	4.18	0	Hydrophobic	false
N1	OE2	GLU- 30	2.62	174.52	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 30	3.38	126.4	H-Bond (Ligand Donor)	false
NAC	OE1	GLU- 30	2.61	165.98	H-Bond (Ligand Donor)	false
NAD	OE2	GLU- 30	3.45	127.07	H-Bond (Ligand Donor)	false
CAB	CD1	PHE- 31	3.6	0	Hydrophobic	false
CAM	CE1	PHE- 31	3.76	0	Hydrophobic	false
CAM	CE2	PHE- 34	3.72	0	Hydrophobic	false
CAL	CZ	PHE- 34	3.62	0	Hydrophobic	false
CAA	SD	MET- 52	4.21	0	Hydrophobic	false
CAA	CG2	THR- 56	3.79	0	Hydrophobic	false
CAG	CB	SER- 59	3.96	0	Hydrophobic	false
CAA	CD1	ILE- 60	4.11	0	Hydrophobic	false
CAA	CD1	LEU- 67	3.87	0	Hydrophobic	false
CAA	CG2	VAL- 115	3.54	0	Hydrophobic	false
NAD	O	HOH- 264	3.06	147.72	H-Bond (Ligand Donor)	false