scPDB - 1i2b entry

Protein Data Bank Entry:

PDB ID : 1i2b

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2001-02-07

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:	15.129
Number of residues:	61
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.095	1056.375

% Hydrophobic	% Polar
42.81	57.19
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	82.32 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
65.2641	88.9556	35.3041

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
O2A	N	TYR- 12	2.89	172.65	H-Bond (Protein Donor)	false
O2N	N	CYS- 13	2.78	165.01	H-Bond (Protein Donor)	false
C5D	CB	CYS- 13	4.31	0	Hydrophobic	false
C3N	SG	CYS- 13	4.45	0	Hydrophobic	false
O3B	OD2	ASP- 32	2.68	163.87	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 32	3.25	132.71	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 32	2.77	156.55	H-Bond (Ligand Donor)	false
N3A	N	ASN- 33	3.29	150.96	H-Bond (Protein Donor)	false
C2B	CG1	VAL- 35	4.2	0	Hydrophobic	false
O2B	N	ARG- 36	3.1	163.06	H-Bond (Protein Donor)	false
C3B	CB	ARG- 36	3.5	0	Hydrophobic	false
N6A	OD2	ASP- 75	2.87	145.6	H-Bond (Ligand Donor)	false
N1A	N	ILE- 76	3.2	168.06	H-Bond (Protein Donor)	false
C5D	CB	PHE- 97	3.75	0	Hydrophobic	false
C4D	CD2	PHE- 97	3.81	0	Hydrophobic	false
O1N	CZ	ARG- 101	3.72	0	Ionic (Protein Cationic)	false
O1N	NE	ARG- 101	2.81	124.86	H-Bond (Protein Donor)	false
C2D	CB	ARG- 101	3.36	0	Hydrophobic	false
N7A	ND2	ASN- 119	3.36	159.57	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 119	2.76	150.24	H-Bond (Ligand Donor)	false
C4D	CB	LEU- 143	4.06	0	Hydrophobic	false
O3D	NZ	LYS- 186	2.78	157.4	H-Bond (Protein Donor)	false
N1N	NE2	GLN- 209	3.29	132.08	H-Bond (Protein Donor)	false
C4N	CG	GLN- 209	4.24	0	Hydrophobic	false
C5N	CB	GLN- 209	3.57	0	Hydrophobic	false
O7N	N	VAL- 212	3.09	165.64	H-Bond (Protein Donor)	false
C4N	CG2	VAL- 212	3.94	0	Hydrophobic	false
O3D	O	HOH- 440	2.7	159.02	H-Bond (Ligand Donor)	false
O2A	O	HOH- 443	2.72	179.98	H-Bond (Protein Donor)	false
O5B	O	HOH- 444	3.24	179.97	H-Bond (Protein Donor)	false
O1A	O	HOH- 620	2.62	176.65	H-Bond (Protein Donor)	false