NPASS Compound

Structure

NPC485622 OpenBabel06302215302D 31 35 0 0 1 0 0 0 0 0999 V2000 -1.6704 2.1848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7079 1.6291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0883 1.9868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5313 1.6291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4938 2.1848 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5313 0.9136 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0883 0.5559 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6966 0.1027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7079 0.9136 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3739 0.6522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5848 -0.0315 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1818 -0.6226 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3504 -1.3817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7613 -1.2051 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3163 -0.2258 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8968 0.8186 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1814 1.1420 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4657 2.9322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1063 0.5005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4135 0.7767 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8063 0.6489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6325 1.3921 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8920 0.2448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1829 1.8639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0092 2.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0660 2.2632 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7787 3.6944 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5080 1.4879 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.2159 -0.3362 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4938 0.3579 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 6 31 1 1 0 0 0 7 29 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 10 1 1 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 23 1 0 0 0 0 12 19 1 0 0 0 0 12 29 1 0 0 0 0 12 13 1 6 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 29 1 0 0 0 0 15 30 1 6 0 0 0 16 17 1 0 0 0 0 16 28 1 1 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 24 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	436.17
Volume:	414.852
LogP:	1.174
LogD:	0.698
LogS:	-4.201
# Rotatable Bonds:	2
TPSA:	136.43
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.43
Synthetic Accessibility Score:	6.531
Fsp3:	0.818
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.416
MDCK Permeability:	7.23334596841596e-05
Pgp-inhibitor:	0.825
Pgp-substrate:	0.049
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.019
30% Bioavailability (F30%):	0.952

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.649
Plasma Protein Binding (PPB):	34.46672439575195%
Volume Distribution (VD):	0.411
Pgp-substrate:	54.271461486816406%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.925
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.493
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.025
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.112
CYP3A4-inhibitor:	0.061
CYP3A4-substrate:	0.243

ADMET: Excretion

Clearance (CL):	2.713
Half-life (T1/2):	0.238

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.353
Drug-inuced Liver Injury (DILI):	0.736
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.289
Maximum Recommended Daily Dose:	0.031
Skin Sensitization:	0.193
Carcinogencity:	0.371
Eye Corrosion:	0.004
Eye Irritation:	0.017
Respiratory Toxicity:	0.926

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC485622

Natural Product ID:	NPC485622
*Common Name:**	OFHVBIQKCNMHKC-ISEFROCLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OFHVBIQKCNMHKC-ISEFROCLSA-N
Standard InCHI:	InChI=1S/C22H28O9/c1-8-5-12(24)17(26)20(4)11(8)6-13-21-7-29-22(28,19(20)21)16(25)9(2)14(21)15(18(27)31-13)30-10(3)23/h5,9,11,13-17,19,25-26,28H,6-7H2,1-4H3/t9-,11+,13-,14-,15-,16-,17-,19-,20-,21+,22-/m1/s1
SMILES:	CC1=CC(=O)[C@H]([C@@]2(C)[C@H]1C[C@@H]1[C@@]34CO[C@]([C@@H]([C@H](C)[C@@H]3[C@H](C(=O)O1)OC(=O)C)O)([C@H]24)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11743733
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0002119] Quassinoids

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO17253	Soulamea soulameoides	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6619884]
NPO17253	Soulamea soulameoides	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6736970]
NPO6324	Soulamea tomentosa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264678]
NPO17253	Soulamea soulameoides	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17253	Soulamea soulameoides	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17253	Soulamea soulameoides	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
EC50	1
ED50	2
GI50	1
IC50	10
Others	4

Activity Type	# Activity
Cell Line	10
NON-MOLECULAR	1
Organism	7

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	200.0	nM	PMID[11754601]
NPT116	Cell Line	HL-60	Homo sapiens	EC50	=	200.0	nM	PMID[11754601]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	500.0	nM	PMID[11754601]
NPT116	Cell Line	HL-60	Homo sapiens	Ratio IC50	=	2.5	n.a.	PMID[11754601]
NPT111	Cell Line	K562	Homo sapiens	IC50	=	1.0	ug.mL-1	PMID[8984156]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	0.5	ug.mL-1	PMID[8984156]
NPT457	Cell Line	BT-549	Homo sapiens	IC50	=	0.3	ug.mL-1	PMID[8984156]
NPT146	Cell Line	SK-OV-3	Homo sapiens	IC50	=	0.5	ug.mL-1	PMID[8984156]
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	=	1.0	ug.mL-1	PMID[8984156]
NPT91	Cell Line	KB	Homo sapiens	ED50	=	6.8	ug ml-1	PMID[7130986]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.01	ug.mL-1	PMID[8984156]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	0.012	ug.mL-1	PMID[8984156]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	GI50	=	30.0	nM	PMID[19199792]
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	0.162	ug.mL-1	DOI[10.1007/s00044-011-9767-1]
NPT14606	ORGANISM	Reticulitermes flavipes	Reticulitermes flavipes	ED50	>	1000.0	ppm	DOI[10.1016/S0926-6690(99)00003-5]
NPT14606	ORGANISM	Reticulitermes flavipes	Reticulitermes flavipes	Inhibition	=	39.36	%	DOI[10.1016/S0926-6690(99)00003-5]
NPT14606	ORGANISM	Reticulitermes flavipes	Reticulitermes flavipes	Activity	=	34.0	%	DOI[10.1016/S0926-6690(99)00003-5]
NPT14606	ORGANISM	Reticulitermes flavipes	Reticulitermes flavipes	Ratio	=	0.7	n.a.	DOI[10.1016/S0926-6690(99)00003-5]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC485622 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	241
0.1-0.2	1378
0.2-0.3	4366
0.3-0.4	7948
0.4-0.5	12027
0.5-0.6	7100
0.6-0.7	5259
0.7-0.8	3666
0.8-0.85	587
0.85-0.9	65
0.9-0.95	40
0.95-1	20

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC485622 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	207
0.1-0.2	1628
0.2-0.3	3834
0.3-0.4	2207
0.4-0.5	711
0.5-0.6	288
0.6-0.7	125
0.7-0.8	129
0.8-0.85	21
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data