scPDB - 3nxx entry

Protein Data Bank Entry:

PDB ID : 3nxx

Resolution :1.350 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:	13.746
Number of residues:	51
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.347	968.625

% Hydrophobic	% Polar
55.75	44.25
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	74.85 %
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
-5.94419	-22.5353	-35.7777

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
O7N	N	ALA- 9	2.86	170.82	H-Bond (Protein Donor)	false
N7N	O	ALA- 9	2.93	161.93	H-Bond (Ligand Donor)	false
C3N	CB	ILE- 16	4.15	0	Hydrophobic	false
N7N	O	ILE- 16	3.06	137.86	H-Bond (Ligand Donor)	false
C3N	CD2	LEU- 22	4.08	0	Hydrophobic	false
C4B	CB	LYS- 54	3.9	0	Hydrophobic	false
C1B	CB	LYS- 54	4.19	0	Hydrophobic	false
O4B	N	LYS- 54	2.99	154.05	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 54	2.72	154.15	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 54	2.72	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 54	3.68	0	Ionic (Protein Cationic)	false
O5B	N	LYS- 55	3.15	155.81	H-Bond (Protein Donor)	false
C5D	CB	LYS- 55	4.02	0	Hydrophobic	false
C5B	CG	LYS- 55	3.97	0	Hydrophobic	false
O2A	OG1	THR- 56	2.69	157.46	H-Bond (Protein Donor)	false
O2A	N	THR- 56	2.81	140.93	H-Bond (Protein Donor)	false
C5N	CG2	THR- 56	3.79	0	Hydrophobic	false
C2D	CB	SER- 59	3.99	0	Hydrophobic	false
O2X	OG	SER- 76	2.61	138.99	H-Bond (Protein Donor)	false
O1X	N	ARG- 77	2.85	161.11	H-Bond (Protein Donor)	false
O1A	N	GLY- 117	3.1	138.09	H-Bond (Protein Donor)	false
O2A	N	GLY- 117	3.23	124.08	H-Bond (Protein Donor)	false
O2N	OG	SER- 118	3.2	147.18	H-Bond (Protein Donor)	false
O2N	N	SER- 118	2.87	159.21	H-Bond (Protein Donor)	false
C4D	CG2	THR- 146	4.23	0	Hydrophobic	false
O3D	O	HOH- 258	2.72	163.6	H-Bond (Ligand Donor)	false
N6A	O	HOH- 341	2.66	157.95	H-Bond (Ligand Donor)	false
N6A	O	HOH- 411	2.92	142.73	H-Bond (Ligand Donor)	false