scPDB - 3pfh entry

Protein Data Bank Entry:

PDB ID : 3pfh

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2010-10-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
ID:	TYLM1_STRFR
AC:	P95748
Organism:	Streptomyces fradiae
Reign:	Bacteria
TaxID:	1906
EC Number:	2.1.1.235

Chains:

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

Ligand binding site composition:

B-Factor:	13.865
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.944	1046.250

% Hydrophobic	% Polar
49.03	50.97
According to VolSite

Ligand :

HET Code:	T3Q
Formula:	C16H26N3O14P2
Molecular weight:	546.337 g/mol
DrugBank ID:	-
Buried Surface Area:	66.66 %
Polar Surface area:	283.77 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-44.583	2.8524	7.8214

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
O4Q	OH	TYR- 14	2.55	173.01	H-Bond (Ligand Donor)	false
C4Q	CZ	TYR- 14	4.49	0	Hydrophobic	false
O1A	NZ	LYS- 29	2.93	160.44	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 29	2.93	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 29	2.9	0	Ionic (Protein Cationic)	false
N3Q	O	PHE- 118	2.85	150.91	H-Bond (Ligand Donor)	false
C2Q	CZ	PHE- 118	4.34	0	Hydrophobic	false
C4'	CH2	TRP- 152	3.82	0	Hydrophobic	false
C2Q	CZ3	TRP- 152	3.84	0	Hydrophobic	false
C5M	CZ2	TRP- 153	4.29	0	Hydrophobic	false
C1'	CE2	TRP- 153	3.8	0	Hydrophobic	false
O4'	NE1	TRP- 153	2.85	138.27	H-Bond (Protein Donor)	false
C2'	CE1	PHE- 158	4.16	0	Hydrophobic	false
O2	N	THR- 159	2.97	159.38	H-Bond (Protein Donor)	false
C5M	CZ	TYR- 162	3.86	0	Hydrophobic	false
C5'	CE1	TYR- 162	3.99	0	Hydrophobic	false
C2'	CD1	TYR- 162	3.5	0	Hydrophobic	false
O2A	NH2	ARG- 177	2.79	143.74	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 177	2.8	142.72	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 177	3.22	0	Ionic (Protein Cationic)	false
O2A	OG	SER- 179	2.56	170.39	H-Bond (Protein Donor)	false
O3'	OG	SER- 181	2.65	164.47	H-Bond (Protein Donor)	false
C3'	CB	SER- 181	3.92	0	Hydrophobic	false
C6Q	CG2	ILE- 190	4.11	0	Hydrophobic	false
C3'	CD1	ILE- 190	4.18	0	Hydrophobic	false
C4Q	CD1	ILE- 212	4.48	0	Hydrophobic	false
C6Q	CD1	ILE- 212	4.46	0	Hydrophobic	false
O1B	CZ	ARG- 241	3.77	0	Ionic (Protein Cationic)	false
O1B	NH2	ARG- 241	2.73	151.13	H-Bond (Protein Donor)	false
O2Q	NH1	ARG- 241	2.85	170.04	H-Bond (Protein Donor)	false