scPDB - 1jkf entry

Protein Data Bank Entry:

PDB ID : 1jkf

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2001-07-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Inositol-3-phosphate synthase
ID:	INO1_YEAST
AC:	P11986
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	5.5.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	31.414
Number of residues:	56
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.209	678.375

% Hydrophobic	% Polar
34.83	65.17
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	70.63 %
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
-19.464	45.1237	8.6395

Binding mode :

What is Poseview ?

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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	ASN- 76	2.74	149.96	H-Bond (Protein Donor)	false
O2N	N	ASN- 77	2.92	170.59	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 148	3.45	169.87	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 148	3.26	171.47	H-Bond (Ligand Donor)	false
N3A	N	ILE- 149	3.49	155.12	H-Bond (Protein Donor)	false
N1A	OG	SER- 184	3.11	158.69	H-Bond (Protein Donor)	false
C3B	CG	GLU- 197	4.21	0	Hydrophobic	false
C1B	CB	ALA- 245	4.11	0	Hydrophobic	false
O3D	O	ALA- 245	3.24	147.34	H-Bond (Ligand Donor)	false
N6A	OD1	ASN- 246	3.3	135.07	H-Bond (Ligand Donor)	false
C3D	CB	SER- 296	4.43	0	Hydrophobic	false
O1N	N	GLY- 409	3.07	152.67	H-Bond (Protein Donor)	false
C5N	CA	GLY- 409	4.32	0	Hydrophobic	false
C4N	CB	ASP- 438	3.54	0	Hydrophobic	false
C3N	CB	ALA- 442	3.76	0	Hydrophobic	false