scPDB - 4fgh entry

Protein Data Bank Entry:

PDB ID : 4fgh

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2012-06-04

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_STAAU
AC:	P0A017
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	20.624
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.460	428.625

% Hydrophobic	% Polar
71.65	28.35
According to VolSite

Ligand :

HET Code:	0U6
Formula:	C30H34N6O3
Molecular weight:	526.629 g/mol
DrugBank ID:	-
Buried Surface Area:	61.39 %
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:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-7.40833	33.6729	-4.35074

Binding mode :

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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	LEU- 5	2.54	154.97	H-Bond (Ligand Donor)	false
N35	O	VAL- 6	3.32	120.23	H-Bond (Ligand Donor)	false
C06	CD2	LEU- 20	4.22	0	Hydrophobic	false
C07	CG	LEU- 20	4.14	0	Hydrophobic	false
C09	CD2	LEU- 20	4.32	0	Hydrophobic	false
C12	CD1	LEU- 20	4.17	0	Hydrophobic	false
C38	CD1	LEU- 20	3.54	0	Hydrophobic	false
N33	OD2	ASP- 27	2.81	146.34	H-Bond (Ligand Donor)	false
N35	OD1	ASP- 27	3.06	147.27	H-Bond (Ligand Donor)	false
N35	OD2	ASP- 27	2.82	141.27	H-Bond (Ligand Donor)	false
C21	CB	LEU- 28	3.61	0	Hydrophobic	false
C23	CD2	LEU- 28	3.25	0	Hydrophobic	false
C38	CD1	LEU- 28	4.44	0	Hydrophobic	false
C39	CG	LEU- 28	3.91	0	Hydrophobic	false
C03	CG2	VAL- 31	4.32	0	Hydrophobic	false
C19	CG1	VAL- 31	4.07	0	Hydrophobic	false
C39	CG2	VAL- 31	4.15	0	Hydrophobic	false
C21	CB	LYS- 32	4.31	0	Hydrophobic	false
C26	CG	LYS- 32	3.97	0	Hydrophobic	false
C25	CB	LYS- 32	3.99	0	Hydrophobic	false
C29	CD	LYS- 32	3.9	0	Hydrophobic	false
C28	CD	LYS- 32	3.75	0	Hydrophobic	false
C09	CB	SER- 49	3.93	0	Hydrophobic	false
C31	CD1	ILE- 50	4.46	0	Hydrophobic	false
C10	CG1	ILE- 50	3.72	0	Hydrophobic	false
C26	CB	LEU- 54	4.31	0	Hydrophobic	false
C19	CD1	LEU- 54	3.5	0	Hydrophobic	false
C27	CG	PRO- 55	3.41	0	Hydrophobic	false
N01	O	PHE- 92	2.86	138.9	H-Bond (Ligand Donor)	false
C04	CZ	PHE- 92	3.38	0	Hydrophobic	false
C31	CZ	PHE- 92	3.34	0	Hydrophobic	false
C09	C2D	NAP- 201	3.39	0	Hydrophobic	false
C04	C4N	NAP- 201	3.41	0	Hydrophobic	false
C06	C5N	NAP- 201	3.88	0	Hydrophobic	false
N35	O	HOH- 306	3.2	145.17	H-Bond (Ligand Donor)	false