scPDB - 3eig entry

Protein Data Bank Entry:

PDB ID : 3eig

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2008-09-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.360	9.120	9.960	1.890	10.420	5

List of CHEMBLId :

CHEMBL34259

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:	12.003
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.116	968.625

% Hydrophobic	% Polar
47.39	52.61
According to VolSite

Ligand :

HET Code:	MTX
Formula:	C20H20N8O5
Molecular weight:	452.423 g/mol
DrugBank ID:	DB00563
Buried Surface Area:	65.89 %
Polar Surface area:	216.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
11.4203	-5.19661	-18.8791

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
NA4	O	ILE- 7	2.91	165.5	H-Bond (Ligand Donor)	false
C9	CD2	LEU- 22	4.34	0	Hydrophobic	false
CM	CG	LEU- 22	3.72	0	Hydrophobic	false
N1	OE2	GLU- 30	2.76	169.87	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 30	3.45	126.76	H-Bond (Ligand Donor)	false
NA2	OE1	GLU- 30	2.66	171.8	H-Bond (Ligand Donor)	false
C12	CG	ARG- 31	4.24	0	Hydrophobic	false
CG	CG	ARG- 31	3.84	0	Hydrophobic	false
C16	CD	ARG- 31	3.51	0	Hydrophobic	false
CG	CB	GLU- 35	3.91	0	Hydrophobic	false
C9	CG2	THR- 56	4.25	0	Hydrophobic	false
CM	CB	SER- 59	3.96	0	Hydrophobic	false
C11	CG2	ILE- 60	4.1	0	Hydrophobic	false
C14	CG1	ILE- 60	3.89	0	Hydrophobic	false
C16	CG	PRO- 61	4.46	0	Hydrophobic	false
O	ND2	ASN- 64	2.85	170.7	H-Bond (Protein Donor)	false
O1	NH2	ARG- 70	2.81	177.28	H-Bond (Protein Donor)	false
O2	NH1	ARG- 70	3.01	162.21	H-Bond (Protein Donor)	false
O1	CZ	ARG- 70	3.69	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 70	3.75	0	Ionic (Protein Cationic)	false
NA4	O	VAL- 115	2.86	133.26	H-Bond (Ligand Donor)	false