scPDB - 1pnv entry

Protein Data Bank Entry:

PDB ID : 1pnv

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2003-06-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-epi-vancosaminyltransferase
ID:	GTFA_AMYOR
AC:	P96558
Organism:	Amycolatopsis orientalis
Reign:	Bacteria
TaxID:	31958
EC Number:	2.4.1.311

Chains:

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

Ligand binding site composition:

B-Factor:	56.915
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.198	1117.125

% Hydrophobic	% Polar
43.20	56.80
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	61.21 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
40.6192	77.2124	25.6443

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
O1B	OG	SER- 10	2.91	143.72	H-Bond (Protein Donor)	false
C1'	CD	ARG- 11	4.41	0	Hydrophobic	false
C4'	CG	ARG- 11	4.38	0	Hydrophobic	false
O1B	N	GLY- 12	3.01	148.26	H-Bond (Protein Donor)	false
C5'	CB	GLU- 15	4.49	0	Hydrophobic	false
C4'	CG	GLU- 15	3.66	0	Hydrophobic	false
C1'	CG	GLU- 15	3.76	0	Hydrophobic	false
O1B	OG	SER- 230	2.83	154.95	H-Bond (Protein Donor)	false
O2B	N	SER- 230	3.06	170.33	H-Bond (Protein Donor)	false
N3	O	VAL- 278	2.72	133.92	H-Bond (Ligand Donor)	false
O4	N	VAL- 278	2.93	134.74	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 280	4.34	0	Hydrophobic	false
O2B	NE2	HIS- 293	3.33	152.25	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 293	3.05	141.08	H-Bond (Protein Donor)	false
O1A	N	THR- 298	3.4	125.38	H-Bond (Protein Donor)	false
O2A	OG1	THR- 298	2.67	159.23	H-Bond (Protein Donor)	false
O2A	N	THR- 298	3.37	145.45	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 301	3.37	0	Hydrophobic	false