NPASS Compound

Structure

NPC268482 OpenBabel06302215072D 46 53 0 0 1 0 0 0 0 0999 V2000 -1.8092 -1.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8957 -1.3468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0867 -1.9346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7912 -0.3522 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4918 0.1568 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8985 1.0703 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3107 1.8794 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7175 2.7929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3162 1.7748 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4269 2.4440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1609 3.2530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4269 3.4440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2930 3.9440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1590 3.4440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1590 4.4440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0250 3.9440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0250 4.9440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8910 5.4440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7571 4.9440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7571 3.9440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2571 3.0779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7571 3.9440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8910 3.4440 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8910 2.4440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0250 1.9440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1590 2.4440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2930 1.9440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2875 1.8394 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0850 0.9658 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0905 0.8613 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.4973 0.0523 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 1.7542 0.2227 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6231 5.4440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4891 4.9440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.3551 5.4440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.2212 4.9440 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.2212 3.9440 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.3551 3.4440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4891 3.9440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0872 3.4440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.0872 5.4440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.3551 6.4440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4891 6.9440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4891 7.9440 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6231 6.4440 0.0000 C 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 6 0 0 0 4 5 1 0 0 0 0 4 32 1 0 0 0 0 5 6 1 1 0 0 0 5 31 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 9 10 1 0 0 0 0 9 30 1 0 0 0 0 10 27 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 26 1 0 0 0 0 14 15 1 0 0 0 0 14 16 1 0 0 0 0 15 16 1 0 0 0 0 16 23 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 34 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 25 1 1 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 33 1 1 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 35 40 1 0 0 0 0 36 37 1 0 0 0 0 36 43 1 0 0 0 0 37 38 1 0 0 0 0 37 42 1 0 0 0 0 38 39 1 0 0 0 0 38 41 1 0 0 0 0 39 40 1 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 44 46 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	644.39
Volume:	653.895
LogP:	4.978
LogD:	4.197
LogS:	-4.721
# Rotatable Bonds:	5
TPSA:	123.91
# H-Bond Aceptor:	9
# H-Bond Donor:	3
# Rings:	8
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.231
Synthetic Accessibility Score:	7.41
Fsp3:	0.919
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.382
MDCK Permeability:	2.3033047909848392e-05
Pgp-inhibitor:	0.141
Pgp-substrate:	0.948
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.641

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	86.904296875%
Volume Distribution (VD):	1.531
Pgp-substrate:	8.29898452758789%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.893
CYP2C19-inhibitor:	0.006
CYP2C19-substrate:	0.513
CYP2C9-inhibitor:	0.069
CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.02
CYP2D6-substrate:	0.216
CYP3A4-inhibitor:	0.545
CYP3A4-substrate:	0.332

ADMET: Excretion

Clearance (CL):	1.122
Half-life (T1/2):	0.36

ADMET: Toxicity

hERG Blockers:	0.839
Human Hepatotoxicity (H-HT):	0.931
Drug-inuced Liver Injury (DILI):	0.118
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.343
Maximum Recommended Daily Dose:	0.924
Skin Sensitization:	0.581
Carcinogencity:	0.021
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.979

Download Data

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

Natural Product: NPC268482

Natural Product ID:	NPC268482
*Common Name:**	SGRPEASUEYQPFC-LQQNVQPXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SGRPEASUEYQPFC-LQQNVQPXSA-N
Standard InCHI:	InChI=1S/C37H56O9/c1-18(2)27-22-15-19(3)29-33(7)13-14-36-17-35(36)12-11-25(44-30-28(43-20(4)38)26(40)21(39)16-42-30)32(5,6)23(35)9-10-24(36)34(33,8)31(41)37(29,45-22)46-27/h19,21-31,39-41H,1,9-17H2,2-8H3/t19-,21-,22-,23+,24+,25+,26+,27-,28-,29-,30+,31-,33-,34-,35-,36+,37+/m1/s1
SMILES:	C=C(C)[C@@H]1[C@H]2C[C@@H](C)[C@@H]3[C@@]4(C)CC[C@]56C[C@]76CC[C@@H](C(C)(C)[C@@H]7CC[C@H]5[C@]4(C)[C@H]([C@@]3(O2)O1)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002321] Cycloartanols and derivatives

*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
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16394543]
NPO22504	Tovomita longifolia	Species	Clusiaceae	Eukaryota	leaves	n.a.	n.a.	PMID[16562847]
NPO20204	Tephrosia candida	Species	Fabaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21510635]
NPO20204	Tephrosia candida	Species	Fabaceae	Eukaryota	aerial parts	Limbe (South West) Province, Cameroon	2007-APR	PMID[21510635]
NPO20898	Agaricus bisporus	Species	Agaricaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO20898	Agaricus bisporus	Species	Agaricaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19967	Calophyllum tomentosum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20898	Agaricus bisporus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20898	Agaricus bisporus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19967	Calophyllum tomentosum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22702	Phytolacca dioica	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21346	Eriocaulon buergerianum	Species	Eriocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21346	Eriocaulon buergerianum	Species	Eriocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20898	Agaricus bisporus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21346	Eriocaulon buergerianum	Species	Eriocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13770	Neurospora santi-florii	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20204	Tephrosia candida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22442	Helix pomatia	Species	Helicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21346	Eriocaulon buergerianum	Species	Eriocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22504	Tovomita longifolia	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21417	Cortinarius evernius	Species	Cortinariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21987	Senecio hygrophilus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26301	Acanthopanax brachypus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO20970	Salvia melissodora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20459	Pfaffia pulverulenta	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21855	Hydrallmania falcata	Species	Sertulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20024	Antennaria cana	Species	Carabidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21656	Pholidota yunnanensis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22310	Pseudodistoma obscurum	Species	Pseudodistomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23102	Siphonaria pectinata	Species	Siphonariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22702	Phytolacca dioica	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20898	Agaricus bisporus	Species	Agaricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4213	Dicranopteris linearis	Species	Gleicheniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19967	Calophyllum tomentosum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22633	Ganoderma carnosum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22959	Eriococcus coriaceus	Species	Eriococcidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22374	Anomala albopilosa	Species	Scarabaeidae	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 NPC268482 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	322
0.1-0.2	2562
0.2-0.3	7546
0.3-0.4	13751
0.4-0.5	7741
0.5-0.6	5496
0.6-0.7	3119
0.7-0.8	1575
0.8-0.85	443
0.85-0.9	138
0.9-0.95	4
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 NPC268482 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	312
0.1-0.2	2714
0.2-0.3	4108
0.3-0.4	1297
0.4-0.5	405
0.5-0.6	248
0.6-0.7	43
0.7-0.8	12
0.8-0.85	3
0.85-0.9	8
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