scPDB - 3nu0 entry

Protein Data Bank Entry:

PDB ID : 3nu0

Resolution :1.350 Å

Experimental Method : X-ray

Deposition Date : 2010-07-06

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_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:	12.512
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.064	448.875

% Hydrophobic	% Polar
57.14	42.86
According to VolSite

Ligand :

HET Code:	3TU
Formula:	C24H19N5O6S
Molecular weight:	505.503 g/mol
DrugBank ID:	-
Buried Surface Area:	61.92 %
Polar Surface area:	208.32 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-11.9564	-7.85692	-0.521972

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
SAU	CG2	ILE- 7	4.31	0	Hydrophobic	false
CAP	CD1	LEU- 22	3.73	0	Hydrophobic	false
N1	OE2	GLU- 30	2.82	179.18	H-Bond (Ligand Donor)	false
NAA	OE1	GLU- 30	2.81	174.41	H-Bond (Ligand Donor)	false
CG	CB	PHE- 31	4.05	0	Hydrophobic	false
CAP	CE1	PHE- 31	3.53	0	Hydrophobic	false
SAU	CE1	PHE- 34	3.47	0	Hydrophobic	false
CB	CB	GLN- 35	3.87	0	Hydrophobic	false
CAH	CG2	THR- 56	3.56	0	Hydrophobic	false
CAH	CG1	ILE- 60	4.12	0	Hydrophobic	false
CAK	CG2	ILE- 60	4.12	0	Hydrophobic	false
CAK	CG	PRO- 61	4.42	0	Hydrophobic	false
O	NH1	ARG- 70	2.96	157.01	H-Bond (Protein Donor)	false
O	NH2	ARG- 70	3.27	140	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 70	2.79	156.6	H-Bond (Protein Donor)	false
O	CZ	ARG- 70	3.59	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 70	3.84	0	Ionic (Protein Cationic)	false
SAU	CB	VAL- 115	3.92	0	Hydrophobic	false
CAL	CB	VAL- 115	3.84	0	Hydrophobic	false
SAU	C4N	NDP- 187	3.59	0	Hydrophobic	false
NAT	O	HOH- 220	3.09	171.66	H-Bond (Ligand Donor)	false
O6	O	HOH- 229	2.85	161.61	H-Bond (Protein Donor)	false
OXT	O	HOH- 268	3.12	147.01	H-Bond (Protein Donor)	false