scPDB - 3sgy entry

Protein Data Bank Entry:

PDB ID : 3sgy

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2011-06-15

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
B	100 %

Ligand binding site composition:

B-Factor:	49.358
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.665	421.875

% Hydrophobic	% Polar
77.60	22.40
According to VolSite

Ligand :

HET Code:	06W
Formula:	C22H23N5O
Molecular weight:	373.451 g/mol
DrugBank ID:	-
Buried Surface Area:	63.72 %
Polar Surface area:	99.94 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
44.5142	-35.4976	-16.3169

Binding mode :

What is Poseview ?

2D View
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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
NAJ	O	LEU- 5	2.62	166.91	H-Bond (Ligand Donor)	false
CAN	CD2	LEU- 20	3.99	0	Hydrophobic	false
CAI	CD1	LEU- 20	3.82	0	Hydrophobic	false
N3	OD2	ASP- 27	3.47	131.58	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 27	2.56	174.17	H-Bond (Ligand Donor)	false
NAH	OD2	ASP- 27	2.81	167.54	H-Bond (Ligand Donor)	false
CAI	CD2	LEU- 28	4.22	0	Hydrophobic	false
C5	CG2	VAL- 31	4.41	0	Hydrophobic	false
CAZ	CG2	VAL- 31	4.05	0	Hydrophobic	false
CAP	SD	MET- 42	4.47	0	Hydrophobic	false
CBB	CE	MET- 42	3.78	0	Hydrophobic	false
CAM	CG2	THR- 46	3.85	0	Hydrophobic	false
CAP	CG2	THR- 46	3.85	0	Hydrophobic	false
CAN	CD1	ILE- 50	3.83	0	Hydrophobic	false
CAP	CD1	ILE- 50	3.48	0	Hydrophobic	false
CAU	CG1	ILE- 50	3.35	0	Hydrophobic	false
CBB	CD2	LEU- 54	3.55	0	Hydrophobic	false
CAR	CD2	LEU- 54	3.35	0	Hydrophobic	false
NAJ	O	PHE- 92	3.08	127.62	H-Bond (Ligand Donor)	false
CAK	CZ	PHE- 92	3.49	0	Hydrophobic	false
CAP	CE1	PHE- 92	3.36	0	Hydrophobic	false
CAL	CE1	PHE- 92	3.53	0	Hydrophobic	false
NAH	OG1	THR- 111	3.31	121.06	H-Bond (Ligand Donor)	false
NAH	O	HOH- 169	2.93	134.63	H-Bond (Ligand Donor)	false
CAL	C4N	NDP- 207	3.56	0	Hydrophobic	false
CAM	C5N	NDP- 207	3.93	0	Hydrophobic	false