scPDB - 3d84 entry

Protein Data Bank Entry:

PDB ID : 3d84

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-05-22

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_MOUSE
AC:	P00375
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	17.461
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.421	860.625

% Hydrophobic	% Polar
55.29	44.71
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	68.3 %
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
1.85307	7.8646	16.806

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	2.94	170.9	H-Bond (Protein Donor)	false
N7N	O	ALA- 9	2.89	134.73	H-Bond (Ligand Donor)	false
C3N	CB	ILE- 16	4.19	0	Hydrophobic	false
N7N	O	ILE- 16	3.21	153.31	H-Bond (Ligand Donor)	false
O3D	O	ASP- 21	3.06	144.43	H-Bond (Ligand Donor)	false
C3N	CD2	LEU- 22	4.2	0	Hydrophobic	false
O4B	N	ARG- 54	2.95	137.28	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 54	2.72	138.35	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 54	3.89	0	Ionic (Protein Cationic)	false
C2B	CB	ARG- 54	3.96	0	Hydrophobic	false
O5B	N	LYS- 55	3.21	149.65	H-Bond (Protein Donor)	false
C5D	CB	LYS- 55	4.1	0	Hydrophobic	false
C5B	CG	LYS- 55	3.77	0	Hydrophobic	false
O1A	OG1	THR- 56	2.69	153.24	H-Bond (Protein Donor)	false
O1A	N	THR- 56	2.79	152.2	H-Bond (Protein Donor)	false
C5N	CG2	THR- 56	3.81	0	Hydrophobic	false
C2D	CB	SER- 59	4.36	0	Hydrophobic	false
O1X	N	ARG- 77	2.84	149.96	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 77	3.66	171.36	Pi/Cation	false
O1N	N	SER- 118	2.77	145.16	H-Bond (Protein Donor)	false
C4D	CG2	THR- 146	3.94	0	Hydrophobic	false
N6A	O	HOH- 229	2.99	165.52	H-Bond (Ligand Donor)	false