NPASS Compound

Structure

NPC107299 OpenBabel06302216092D 29 30 0 0 1 0 0 0 0 0999 V2000 4.0443 -1.4798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2957 -0.8166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4958 0.1631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3472 -1.1333 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0351 -0.6398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5294 -0.3478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9460 -0.3243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9298 -1.3242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0261 -1.6178 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.1588 -2.1717 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6863 -2.7062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5718 -2.2415 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6461 -3.7054 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5800 -2.5762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0800 -3.4422 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1409 -2.7387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7130 -2.6219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1417 -3.5253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1653 -2.2526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9648 -2.8533 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3942 -1.7154 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3813 -1.8758 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7359 -2.8108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1034 -3.5854 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7229 -2.9712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1006 -3.7379 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6007 -0.7994 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2937 0.9559 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 4 2 1 1 0 0 0 4 5 1 0 0 0 0 4 21 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 28 1 0 0 0 0 7 8 2 0 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 27 1 0 0 0 0 10 11 1 6 0 0 0 10 14 1 0 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 2 0 0 0 0 16 26 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 6 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	438.3
Volume:	474.595
LogP:	2.28
LogD:	1.634
LogS:	-4.144
# Rotatable Bonds:	8
TPSA:	107.22
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.34
Synthetic Accessibility Score:	5.139
Fsp3:	0.72
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.531
MDCK Permeability:	0.0003513378032948822
Pgp-inhibitor:	0.002
Pgp-substrate:	0.156
Human Intestinal Absorption (HIA):	0.06
20% Bioavailability (F20%):	0.921
30% Bioavailability (F30%):	0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.147
Plasma Protein Binding (PPB):	59.27188491821289%
Volume Distribution (VD):	1.288
Pgp-substrate:	40.612205505371094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.037
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.055
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.296
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.076
CYP3A4-inhibitor:	0.086
CYP3A4-substrate:	0.246

ADMET: Excretion

Clearance (CL):	7.376
Half-life (T1/2):	0.526

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.926
Drug-inuced Liver Injury (DILI):	0.042
AMES Toxicity:	0.045
Rat Oral Acute Toxicity:	0.087
Maximum Recommended Daily Dose:	0.98
Skin Sensitization:	0.181
Carcinogencity:	0.933
Eye Corrosion:	0.003
Eye Irritation:	0.026
Respiratory Toxicity:	0.085

Download Data

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

Natural Product: NPC107299

Natural Product ID:	NPC107299
*Common Name:**	KFOAFRGWCVUHFY-XPIXLHGCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KFOAFRGWCVUHFY-XPIXLHGCSA-N
Standard InCHI:	InChI=1S/C22H26O7/c1-10(2)15-8-7-14-9-16(29-22(14)27)17(11(3)4)20(26)18(24)12(5)19(25)21(15)28-13(6)23/h9,15-17,21,24H,1,3,7-8H2,2,4-6H3/b18-12+/t15-,16+,17+,21-/m0/s1
SMILES:	C=C(C)[C@@H]1CCC2=C[C@H]([C@@H](C(=C)C)C(=O)/C(=C(/C)C(=O)[C@H]1OC(=O)C)/O)OC2=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11704081
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

*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
NPO15684	Cochliobolus heterostrophus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10395513]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15182859]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	root	n.a.	PMID[16310231]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	root	n.a.	PMID[16651783]
NPO24654	Curculigo crassifolia	Species	Hypoxidaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[18958422]
NPO25042	Fusarium tricinctum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21090694]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	stem	n.a.	PMID[21428375]
NPO25544	Encyclia michuacana	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21510636]
NPO23799	Gentiana triflora	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23599008]
NPO25042	Fusarium tricinctum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24175613]
NPO20005	Penstemon barbatus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26351040]
NPO1448	Diospyros lycioides	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9644074]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO23799	Gentiana triflora	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20275	Juniperus sabina	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8735	Berberis poiretii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8735	Berberis poiretii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23799	Gentiana triflora	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24562	Saussurea petrovii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20275	Juniperus sabina	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25042	Fusarium tricinctum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18878.1	Amaranthus blitum subsp. oleraceus	Subspecies	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23799	Gentiana triflora	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20275	Juniperus sabina	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO23799	Gentiana triflora	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8735	Berberis poiretii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15326	Paranemertes peregrina	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19851	Miconia stenostachya	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20005	Penstemon barbatus	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25930	Cystoseira balearica	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25544	Encyclia michuacana	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26421	Urtica laetevirens	Species	Urticaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18873.7	Salmonella enterica subsp. enterica serovar typhi	Subspecies	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23799	Gentiana triflora	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17597	Cassia fistulosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20129	Salicornia europaea	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25527	Tephrosia multijuga	Species	Geometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25442	Isocoma tenuisecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24654	Curculigo crassifolia	Species	Hypoxidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8735	Berberis poiretii	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24562	Saussurea petrovii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25042	Fusarium tricinctum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24985	Lippia asperifolia	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3843	Rhododendron metternichii	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18878.1	Amaranthus blitum subsp. oleraceus	Subspecies	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1448	Diospyros lycioides	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12235	Trachelospermum jasminoides	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21476	Pterogorgia kallos	Species	Gorgoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24741	Psathyrella scobinacea	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24787	Astragalus babatagi	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21817	Riccardia chamedryfolia	Species	Aneuraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15684	Cochliobolus heterostrophus	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20275	Juniperus sabina	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24210	Senecio heterotrichus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24474	Rhododendron lepidotum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24928	Cratoxylum cochinchinense	Species	Hypericaceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC107299 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	198
0.1-0.2	1216
0.2-0.3	4966
0.3-0.4	10043
0.4-0.5	15025
0.5-0.6	6803
0.6-0.7	3446
0.7-0.8	942
0.8-0.85	56
0.85-0.9	1
0.9-0.95	1
0.95-1	0

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 NPC107299 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	181
0.1-0.2	1812
0.2-0.3	3615
0.3-0.4	2285
0.4-0.5	870
0.5-0.6	294
0.6-0.7	87
0.7-0.8	6
0.8-0.85	0
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