scPDB - 3vcy entry

Protein Data Bank Entry:

PDB ID : 3vcy

Resolution :1.930 Å

Experimental Method : X-ray

Deposition Date : 2012-01-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine 1-carboxyvinyltransferase
ID:	MURA_VIBFM
AC:	B5F9P4
Organism:	Vibrio fischeri
Reign:	Bacteria
TaxID:	388396
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.474
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.784	1046.250

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	59 %
Polar Surface area:	325.69 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
23.3143	20.0712	22.2751

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
O3'	ND2	ASN- 24	3.29	136.22	H-Bond (Protein Donor)	false
C8'	CD1	LEU- 27	4.32	0	Hydrophobic	false
C8'	CB	ALA- 93	4.2	0	Hydrophobic	false
C8'	CH2	TRP- 96	3.54	0	Hydrophobic	false
O2B	CZ	ARG- 121	3.98	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 121	3	164.75	H-Bond (Protein Donor)	false
N3	OD1	ASP- 124	2.9	155.41	H-Bond (Ligand Donor)	false
O4	N	LEU- 125	2.85	145.22	H-Bond (Protein Donor)	false
O1A	OG	SER- 163	2.51	169.28	H-Bond (Protein Donor)	false
C1'	CB	VAL- 164	4.17	0	Hydrophobic	false
C6'	CG2	VAL- 164	4.24	0	Hydrophobic	false
O2A	N	VAL- 164	2.83	150.34	H-Bond (Protein Donor)	false
O1B	N	GLY- 165	2.9	120.78	H-Bond (Protein Donor)	false
C6'	CG2	THR- 305	3.94	0	Hydrophobic	false
O3'	OD2	ASP- 306	3.03	153.37	H-Bond (Ligand Donor)	false
O4'	OD1	ASP- 306	2.63	153.65	H-Bond (Ligand Donor)	false
C6'	CG2	ILE- 328	4.25	0	Hydrophobic	false
C5B	CG2	ILE- 328	3.76	0	Hydrophobic	false
O3B	O	ILE- 328	2.88	165.85	H-Bond (Ligand Donor)	false
C4'	CE2	PHE- 329	4.36	0	Hydrophobic	false
C5'	CZ	PHE- 329	4.18	0	Hydrophobic	false
C6'	CE2	PHE- 329	4.27	0	Hydrophobic	false
C3B	CE1	PHE- 329	4.02	0	Hydrophobic	false