scPDB - 1kvt entry

Protein Data Bank Entry:

PDB ID : 1kvt

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 1997-03-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-glucose 4-epimerase
ID:	GALE_ECOLI
AC:	P09147
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	5.1.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	26.469
Number of residues:	42
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.184	1150.875

% Hydrophobic	% Polar
51.32	48.68
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	70.59 %
Polar Surface area:	316.82 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:	9

Mass center Coordinates

X	Y	Z
66.5234	10.8836	53.0046

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
C3'	CG2	VAL- 124	4.37	0	Hydrophobic	false
C4'	CB	VAL- 124	4.36	0	Hydrophobic	false
C6'	CG2	VAL- 124	3.58	0	Hydrophobic	false
C6'	CB	ALA- 125	3.84	0	Hydrophobic	false
C3'	CE2	TYR- 149	4.18	0	Hydrophobic	false
O3'	OH	TYR- 149	3.48	125.49	H-Bond (Ligand Donor)	false
O1B	ND2	ASN- 179	3.16	164.39	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 199	3.08	159.16	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 199	2.85	150.06	H-Bond (Protein Donor)	false
C1C	CD1	LEU- 200	4.41	0	Hydrophobic	false
C4C	CD2	LEU- 200	4.24	0	Hydrophobic	false
C5C	CB	LEU- 200	4.25	0	Hydrophobic	false
O2A	N	LEU- 200	3.16	161.45	H-Bond (Protein Donor)	false
N3	O	ALA- 216	2.69	169.76	H-Bond (Ligand Donor)	false
O2	N	PHE- 218	2.85	165.55	H-Bond (Protein Donor)	false
O1B	NE	ARG- 231	2.72	154.26	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 231	3.79	0	Ionic (Protein Cationic)	false
C4C	CG	ARG- 231	4.12	0	Hydrophobic	false
C5C	CZ	TYR- 233	4.45	0	Hydrophobic	false
C1C	CG2	VAL- 269	3.91	0	Hydrophobic	false
C4C	CG2	VAL- 269	4.47	0	Hydrophobic	false
O5C	NH2	ARG- 292	3.44	123.18	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 292	2.73	165.81	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 292	3.2	134.97	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 292	3.42	0	Ionic (Protein Cationic)	false
O6'	OH	TYR- 299	2.67	158.62	H-Bond (Protein Donor)	false
C4'	C4N	NAD- 340	3.66	0	Hydrophobic	false