scPDB - 1wvg entry

Protein Data Bank Entry:

PDB ID : 1wvg

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2004-12-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CDP-glucose 4,6-dehydratase
ID:	RFBG_SALTY
AC:	P26397
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	4.2.1.45

Chains:

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

Ligand binding site composition:

B-Factor:	29.142
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.232	664.875

% Hydrophobic	% Polar
40.10	59.90
According to VolSite

Ligand :

HET Code:	CXY
Formula:	C14H21N3O15P2
Molecular weight:	533.275 g/mol
DrugBank ID:	DB03069
Buried Surface Area:	76.03 %
Polar Surface area:	305.87 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
65.0554	21.4159	54.9488

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
O2'	O	PRO- 93	3.38	154.49	H-Bond (Ligand Donor)	false
O3'	O	PRO- 93	2.74	176.47	H-Bond (Ligand Donor)	false
O4'	OG	SER- 134	2.87	165.26	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 136	2.81	138.87	H-Bond (Protein Donor)	false
O1'	NZ	LYS- 136	3.16	130.39	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 136	2.81	0	Ionic (Protein Cationic)	false
O4'	OH	TYR- 159	2.89	157.14	H-Bond (Ligand Donor)	false
C3'	CE2	TYR- 159	3.98	0	Hydrophobic	false
O1B	ND2	ASN- 197	2.84	165.82	H-Bond (Protein Donor)	false
C2'	CD	ARG- 208	4.28	0	Hydrophobic	false
O2'	NE	ARG- 208	2.87	148.01	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 208	3.46	127.78	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 208	3.49	131.6	H-Bond (Protein Donor)	false
O1A	N	LEU- 209	3.04	162.08	H-Bond (Protein Donor)	false
N4	OD2	ASP- 212	2.82	165.47	H-Bond (Ligand Donor)	false
N4	O	ILE- 224	2.81	164.03	H-Bond (Ligand Donor)	false
N3	N	ARG- 226	3.1	175.49	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 227	2.7	153.19	H-Bond (Protein Donor)	false
O2	N	ASN- 227	2.55	154.72	H-Bond (Protein Donor)	false
C1D	CB	ASN- 227	4.38	0	Hydrophobic	false
O1B	NE	ARG- 232	2.97	163.8	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 232	3.93	0	Ionic (Protein Cationic)	false
C5D	CG	ARG- 232	4.09	0	Hydrophobic	false
C5D	CH2	TRP- 234	3.86	0	Hydrophobic	false
C4D	CG2	VAL- 274	3.92	0	Hydrophobic	false
C1D	CG2	VAL- 274	3.94	0	Hydrophobic	false
O2D	OE2	GLU- 301	2.8	150.35	H-Bond (Ligand Donor)	false
O4'	O	HOH- 2536	2.98	154.38	H-Bond (Protein Donor)	false
O2A	O	HOH- 2709	2.8	160.76	H-Bond (Protein Donor)	false