scPDB - 1i24 entry

Protein Data Bank Entry:

PDB ID : 1i24

Resolution :1.200 Å

Experimental Method : X-ray

Deposition Date : 2001-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-sulfoquinovose synthase, chloroplastic
ID:	SQD1_ARATH
AC:	O48917
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	3.13.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	9.976
Number of residues:	56
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.838	621.000

% Hydrophobic	% Polar
46.20	53.80
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	79.87 %
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
71.0844	98.6516	26.2132

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	ARG- 101	3.27	160.69	H-Bond (Ligand Donor)	false
O3'	O	ARG- 101	2.76	167.38	H-Bond (Ligand Donor)	false
O2'	NH2	ARG- 101	2.88	135.82	H-Bond (Protein Donor)	false
C2'	CD	ARG- 101	4.08	0	Hydrophobic	false
C4'	CB	THR- 145	4.44	0	Hydrophobic	false
O4'	OG1	THR- 145	2.52	120.12	H-Bond (Ligand Donor)	false
O4'	OH	TYR- 182	2.64	151.32	H-Bond (Protein Donor)	false
C3'	CE2	TYR- 182	3.55	0	Hydrophobic	false
O6'	O	GLN- 209	3.36	142.96	H-Bond (Ligand Donor)	false
C5C	CG2	VAL- 211	4.49	0	Hydrophobic	false
C1'	CG2	VAL- 211	4.41	0	Hydrophobic	false
C6'	CG2	VAL- 211	4.16	0	Hydrophobic	false
C1'	CG2	THR- 238	3.89	0	Hydrophobic	false
O2A	N	ALA- 239	2.79	156.42	H-Bond (Protein Donor)	false
O4	NE	ARG- 242	2.87	163.21	H-Bond (Protein Donor)	false
O4	NH2	ARG- 242	3.19	138.6	H-Bond (Protein Donor)	false
N3	O	THR- 254	2.82	166.35	H-Bond (Ligand Donor)	false
O4	OG1	THR- 254	2.9	138.94	H-Bond (Protein Donor)	false
O2	N	TYR- 256	3	161	H-Bond (Protein Donor)	false
C2C	CD2	TYR- 256	4.04	0	Hydrophobic	false
C5C	CG	ARG- 263	4.37	0	Hydrophobic	false
C1C	CG2	VAL- 300	3.84	0	Hydrophobic	false
C4C	CG2	VAL- 300	4.4	0	Hydrophobic	false
C2C	CD	ARG- 327	4.23	0	Hydrophobic	false
O1A	CZ	ARG- 327	3.73	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 327	3.49	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 327	2.92	129.34	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 327	2.79	156.77	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 327	3.35	130.22	H-Bond (Protein Donor)	false
O2C	OE2	GLU- 329	2.68	144.96	H-Bond (Ligand Donor)	false
O3C	OE1	GLU- 329	2.74	170.9	H-Bond (Ligand Donor)	false
C2'	C3N	NAD- 401	4.08	0	Hydrophobic	false
C3'	C4N	NAD- 401	4.4	0	Hydrophobic	false
C4'	C5N	NAD- 401	3.58	0	Hydrophobic	false
C5'	C4N	NAD- 401	4.17	0	Hydrophobic	false
C6'	C5N	NAD- 401	3.83	0	Hydrophobic	false
O3'	O2D	NAD- 401	2.83	170.33	H-Bond (Protein Donor)	false
O2B	O	HOH- 460	2.74	171.4	H-Bond (Protein Donor)	false