NPASS Compound

Structure

NPC287074 OpenBabel06302216122D 36 40 0 0 1 0 0 0 0 0999 V2000 -3.2402 -0.4275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3209 -0.6736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0743 -1.5927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7471 -2.2658 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6482 -0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6485 0.9512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8251 1.4275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9516 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8243 1.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6491 0.9521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6493 0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3422 0.9784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8248 -0.4759 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8251 -1.4281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6499 -1.9040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4744 -1.4276 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.2987 -1.9035 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4524 -2.3927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2992 -2.8552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1237 -3.3306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9477 -2.8543 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.9471 -1.9025 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9339 -1.9020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1226 -1.4271 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1223 -0.4749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2981 0.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4742 -0.4754 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4739 0.5021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4400 -1.0477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4268 -1.0471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9461 -0.1934 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8025 -3.3472 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0005 1.9033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8687 2.2906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7706 2.4624 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 2 5 1 0 0 0 0 3 4 1 0 0 0 0 5 6 1 0 0 0 0 5 33 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 33 1 0 0 0 0 8 9 1 0 0 0 0 8 34 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 27 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 13 33 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 27 1 0 0 0 0 17 24 1 0 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 21 22 1 0 0 0 0 21 32 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 22 29 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	502.33
Volume:	529.486
LogP:	2.54
LogD:	3.204
LogS:	-3.138
# Rotatable Bonds:	4
TPSA:	115.06
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.396
Synthetic Accessibility Score:	5.005
Fsp3:	0.867
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:	-5.715
MDCK Permeability:	9.535027857054956e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.932
30% Bioavailability (F30%):	0.13

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.047
Plasma Protein Binding (PPB):	85.08142852783203%
Volume Distribution (VD):	0.51
Pgp-substrate:	7.64773416519165%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.346
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.759
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.122
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.123
CYP3A4-inhibitor:	0.056
CYP3A4-substrate:	0.066

ADMET: Excretion

Clearance (CL):	1.387
Half-life (T1/2):	0.731

ADMET: Toxicity

hERG Blockers:	0.049
Human Hepatotoxicity (H-HT):	0.295
Drug-inuced Liver Injury (DILI):	0.015
AMES Toxicity:	0.013
Rat Oral Acute Toxicity:	0.243
Maximum Recommended Daily Dose:	0.705
Skin Sensitization:	0.19
Carcinogencity:	0.019
Eye Corrosion:	0.332
Eye Irritation:	0.844
Respiratory Toxicity:	0.947

Download Data

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

Natural Product: NPC287074

Natural Product ID:	NPC287074
*Common Name:**	YOTJBGVSVFKNEU-LMSCMDSGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YOTJBGVSVFKNEU-LMSCMDSGSA-N
Standard InCHI:	InChI=1S/C30H46O6/c1-17(16-31)18-8-13-30(25(35)36)15-14-27(3)19(23(18)30)6-7-20-26(2)11-10-22(32)29(5,24(33)34)21(26)9-12-28(20,27)4/h18-23,31-32H,1,6-16H2,2-5H3,(H,33,34)(H,35,36)/t18-,19+,20+,21+,22+,23+,26+,27+,28+,29+,30-/m0/s1
SMILES:	C=C(CO)[C@@H]1CC[C@@]2(CC[C@]3(C)[C@H](CC[C@@H]4[C@@]5(C)CC[C@H]([C@@](C)([C@@H]5CC[C@@]34C)C(=O)O)O)[C@@H]12)C(=O)O
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:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[16792421]
NPO14784	Hydnocarpus wightiana	Species	Achariaceae	Eukaryota	seeds	n.a.	n.a.	PMID[1800632]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	whole plants	Panshi, Jilin Province, China	2009-JUN	PMID[21534540]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21534540]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25453801]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26702644]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28383891]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14784	Hydnocarpus wightiana	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17753	Carex kobomugi	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14784	Hydnocarpus wightiana	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17369	Onobrychis bobrovi	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7413	Wedelia biflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25947	Bejaranoa semistriata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25041	Virola bicuhyba	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17087	Plagiomnium affine	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15212	Fraxinus chinensis	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9931	Cryptocarya caloneura	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9501	Melaleuca leucadendron	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12155	Wrightia mollissima	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27844	Coreopsis verticillata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15889	Campanula biebersteiniana	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1804	Grevillea pyramidalis	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11738	Talaromyces emodensis	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17753	Carex kobomugi	Species	Cyperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14532	Salmea scandens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14784	Hydnocarpus wightiana	Species	Achariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29294	Rotheca myricoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7990	Salsola somalensis	Species	Chenopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6000	Helichrysum panduratum	Species	Asteraceae	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 NPC287074 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	201
0.1-0.2	1626
0.2-0.3	5845
0.3-0.4	15016
0.4-0.5	7379
0.5-0.6	5164
0.6-0.7	4798
0.7-0.8	2259
0.8-0.85	331
0.85-0.9	48
0.9-0.95	23
0.95-1	7

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 NPC287074 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	182
0.1-0.2	2002
0.2-0.3	4054
0.3-0.4	1980
0.4-0.5	481
0.5-0.6	176
0.6-0.7	194
0.7-0.8	76
0.8-0.85	3
0.85-0.9	1
0.9-0.95	1
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