scPDB - 4m7v entry

Protein Data Bank Entry:

PDB ID : 4m7v

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2013-08-12

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:	Q834R2_ENTFA
AC:	Q834R2
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.906
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.984	344.250

% Hydrophobic	% Polar
67.65	32.35
According to VolSite

Ligand :

HET Code:	RAR
Formula:	C27H30N6O3
Molecular weight:	486.565 g/mol
DrugBank ID:	-
Buried Surface Area:	53.3 %
Polar Surface area:	128.95 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
24.9156	-13.7517	10.2375

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
N01	O	ILE- 5	2.89	160.59	H-Bond (Ligand Donor)	false
C06	CD2	LEU- 20	3.91	0	Hydrophobic	false
C09	CG	LEU- 20	3.69	0	Hydrophobic	false
C12	CD1	LEU- 20	4.05	0	Hydrophobic	false
C07	CD1	LEU- 20	3.79	0	Hydrophobic	false
N33	OD2	ASP- 27	2.82	157.69	H-Bond (Ligand Donor)	false
N35	OD1	ASP- 27	2.56	165.99	H-Bond (Ligand Donor)	false
N35	OD2	ASP- 27	3.44	129.08	H-Bond (Ligand Donor)	false
C12	CD1	LEU- 28	4.48	0	Hydrophobic	false
C23	CB	LEU- 28	3.66	0	Hydrophobic	false
C15	CD2	LEU- 28	3.6	0	Hydrophobic	false
C23	CD	LYS- 29	4.42	0	Hydrophobic	false
C04	CE2	PHE- 31	4.19	0	Hydrophobic	false
C14	CE1	PHE- 31	3.8	0	Hydrophobic	false
C15	CD1	PHE- 31	4.39	0	Hydrophobic	false
C19	CD1	PHE- 31	4.05	0	Hydrophobic	false
C26	CB	LYS- 32	3.55	0	Hydrophobic	false
C09	CG	MET- 50	4.07	0	Hydrophobic	false
C07	CG	MET- 50	3.91	0	Hydrophobic	false
C14	CE	MET- 50	4.07	0	Hydrophobic	false
C14	CD1	LEU- 55	4.21	0	Hydrophobic	false
C19	CD1	LEU- 55	4.24	0	Hydrophobic	false
C24	CD2	LEU- 55	3.81	0	Hydrophobic	false
C28	CG	PRO- 56	3.91	0	Hydrophobic	false
N01	O	GLY- 97	2.75	128.93	H-Bond (Ligand Donor)	false
C06	C3N	NAP- 201	4.49	0	Hydrophobic	false
C04	C3N	NAP- 201	3.54	0	Hydrophobic	false