NPASS Compound

Structure

NPC187508 OpenBabel06302215162D 27 28 0 0 1 0 0 0 0 0999 V2000 -3.2321 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2321 -1.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2321 -2.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7321 -3.7321 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5411 -0.5878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2321 -1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3366 -2.5334 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5276 -3.1211 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2321 -1.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9230 -0.5878 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1456 -1.9456 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4921 -0.2788 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 1 0 0 0 3 5 1 0 0 0 0 3 7 1 0 0 0 0 5 6 3 0 0 0 0 8 7 1 1 0 0 0 8 9 1 0 0 0 0 8 24 1 0 0 0 0 9 10 1 0 0 0 0 9 27 1 6 0 0 0 10 11 1 0 0 0 0 10 26 1 1 0 0 0 11 12 1 0 0 0 0 11 25 1 6 0 0 0 12 13 1 1 0 0 0 12 24 1 0 0 0 0 13 14 1 0 0 0 0 15 14 1 1 0 0 0 15 16 1 0 0 0 0 15 21 1 0 0 0 0 16 17 1 0 0 0 0 16 23 1 6 0 0 0 17 18 1 0 0 0 0 17 20 1 0 0 0 0 17 22 1 6 0 0 0 18 19 1 0 0 0 0 20 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	393.16
Volume:	361.805
LogP:	-1.095
LogD:	-1.834
LogS:	-1.437
# Rotatable Bonds:	7
TPSA:	182.09
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	2
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.258
Synthetic Accessibility Score:	4.946
Fsp3:	0.938
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.113
MDCK Permeability:	0.0001172748306998983
Pgp-inhibitor:	0.003
Pgp-substrate:	0.935
Human Intestinal Absorption (HIA):	0.882
20% Bioavailability (F20%):	0.853
30% Bioavailability (F30%):	0.924

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.199
Plasma Protein Binding (PPB):	18.655805587768555%
Volume Distribution (VD):	0.403
Pgp-substrate:	74.4900894165039%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.971
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.076
CYP2C9-inhibitor:	0.0
CYP2C9-substrate:	0.013
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.043
CYP3A4-inhibitor:	0.014
CYP3A4-substrate:	0.039

ADMET: Excretion

Clearance (CL):	1.134
Half-life (T1/2):	0.815

ADMET: Toxicity

hERG Blockers:	0.062
Human Hepatotoxicity (H-HT):	0.072
Drug-inuced Liver Injury (DILI):	0.615
AMES Toxicity:	0.407
Rat Oral Acute Toxicity:	0.755
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.86
Carcinogencity:	0.133
Eye Corrosion:	0.005
Eye Irritation:	0.066
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC187508

Natural Product ID:	NPC187508
*Common Name:**	MTXHSRQBZHUBTP-OUIBXEOXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MTXHSRQBZHUBTP-OUIBXEOXSA-N
Standard InCHI:	InChI=1S/C16H27NO10/c1-3-15(2,5-17)27-13-11(21)10(20)9(19)8(26-13)4-24-14-12(22)16(23,6-18)7-25-14/h8-14,18-23H,3-4,6-7H2,1-2H3/t8-,9-,10+,11-,12+,13+,14-,15+,16-/m1/s1
SMILES:	CC[C@@](C)(C#N)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@@](CO)(CO2)O)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002365] Cyanogenic glycosides

*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
NPO8584	Schisandra arisanensis	Species	Schisandraceae	Eukaryota	fruits	n.a.	n.a.	PMID[19673515]
NPO8584	Schisandra arisanensis	Species	Schisandraceae	Eukaryota	fruits	n.a.	n.a.	PMID[20536188]
NPO8584	Schisandra arisanensis	Species	Schisandraceae	Eukaryota	fruits	n.a.	n.a.	PMID[23265871]
NPO20288	Polytolypa hystricis	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8691217]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota	Tubers	n.a.		Database[FooDB]
NPO20846	Sophora japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8584	Schisandra arisanensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19139	Senecio polyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8198	Podocarpus montanus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8198	Podocarpus montanus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20846	Sophora japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22294	Pteris inaequalis	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8584	Schisandra arisanensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19139	Senecio polyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15478	Senna sophera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8198	Podocarpus montanus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20846	Sophora japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20846	Sophora japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19139	Senecio polyodon	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28078	Melaleuca decora	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21101	Felicia amelloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22599	Crataegus pontica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16711	Baccharis solieri	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23952	Phlomoides medicinalis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22871	Aster alpinus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21951	Paramignya griffithii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8584	Schisandra arisanensis	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20592	Rhodoglossum japonicum	Species	Gigartinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21368	Tricholoma batschii	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23353	[polyangium] brachysporum	Species	n.a.	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO21582	Manihot esculenta	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22529	Calceolaria thyrsiflora	Species	Calceolariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20288	Polytolypa hystricis	Species	Onygenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20846	Sophora japonica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15478	Senna sophera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20015	Echinocystis lobata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22711	Athanasia dregeana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22294	Pteris inaequalis	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21530	Arnica viscosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22650	Helenium quadridentatum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28627.1	Coptis trifolia subsp. groenlandica	Subspecies	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23025	Roccellaria mollis	Species	Roccellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21822	Berberis crataegina	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8198	Podocarpus montanus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22927	Xanthoparmelia pokornyi	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18684	Calophyllum thwaitesii	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22812	Acacia cambagei	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11064	Haemanthus toxicarius	Species	Amaryllidaceae	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 NPC187508 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	370
0.1-0.2	7823
0.2-0.3	17964
0.3-0.4	10625
0.4-0.5	4737
0.5-0.6	1024
0.6-0.7	129
0.7-0.8	20
0.8-0.85	2
0.85-0.9	3
0.9-0.95	0
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 NPC187508 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	347
0.1-0.2	5153
0.2-0.3	2624
0.3-0.4	676
0.4-0.5	244
0.5-0.6	75
0.6-0.7	23
0.7-0.8	5
0.8-0.85	3
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