NPASS Compound

Structure

NPC207057 OpenBabel06302215192D 30 33 0 0 1 0 0 0 0 0999 V2000 3.2862 -3.9980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3105 -3.9983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8229 -4.8434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8225 -3.1535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9773 -2.6659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9776 -3.6415 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3101 -2.3083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8220 -1.4635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8463 -1.4638 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3587 -2.3089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8460 -0.4881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6906 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6903 0.9766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9761 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8463 1.4642 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8466 2.4409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6926 2.9290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5383 2.4404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3837 2.9285 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2289 2.4399 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2286 1.4632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3832 0.9751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5380 1.4637 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5377 0.4637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6920 0.9756 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6917 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8457 -0.4886 0.0000 C 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 0.0003 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0951 2.9395 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 4 1 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 4 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 1 0 0 0 11 9 1 6 0 0 0 11 12 1 0 0 0 0 11 28 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 28 1 0 0 0 0 15 16 1 1 0 0 0 15 25 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 23 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 20 30 1 6 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 23 25 1 0 0 0 0 25 26 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	412.37
Volume:	479.432
LogP:	7.849
LogD:	6.326
LogS:	-6.801
# Rotatable Bonds:	5
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.454
Synthetic Accessibility Score:	4.545
Fsp3:	0.862
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.684
MDCK Permeability:	9.881415280688088e-06
Pgp-inhibitor:	0.968
Pgp-substrate:	0.004
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.977
30% Bioavailability (F30%):	0.098

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.289
Plasma Protein Binding (PPB):	95.81224822998047%
Volume Distribution (VD):	1.991
Pgp-substrate:	1.446197271347046%

ADMET: Metabolism

CYP1A2-inhibitor:	0.103
CYP1A2-substrate:	0.622
CYP2C19-inhibitor:	0.103
CYP2C19-substrate:	0.951
CYP2C9-inhibitor:	0.238
CYP2C9-substrate:	0.631
CYP2D6-inhibitor:	0.12
CYP2D6-substrate:	0.878
CYP3A4-inhibitor:	0.605
CYP3A4-substrate:	0.391

ADMET: Excretion

Clearance (CL):	6.636
Half-life (T1/2):	0.028

ADMET: Toxicity

hERG Blockers:	0.725
Human Hepatotoxicity (H-HT):	0.273
Drug-inuced Liver Injury (DILI):	0.363
AMES Toxicity:	0.002
Rat Oral Acute Toxicity:	0.009
Maximum Recommended Daily Dose:	0.758
Skin Sensitization:	0.955
Carcinogencity:	0.22
Eye Corrosion:	0.874
Eye Irritation:	0.71
Respiratory Toxicity:	0.785

Download Data

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

Natural Product: NPC207057

Natural Product ID:	NPC207057
*Common Name:**	CGUJNZGCCXPWEZ-OHPSOFBHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CGUJNZGCCXPWEZ-OHPSOFBHSA-N
Standard InCHI:	InChI=1S/C29H48O/c1-19(2)27(4,5)15-12-20(3)24-10-11-25-23-9-8-21-18-22(30)13-16-28(21,6)26(23)14-17-29(24,25)7/h8,20,22-26,30H,1,9-18H2,2-7H3/t20-,22+,23+,24-,25+,26+,28+,29-/m1/s1
SMILES:	C=C(C)C(C)(C)CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	14312353
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0003567] Ergostane steroids [CHEMONTID:0001403] Ergosterols 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
NPO737	Aspergillus japonicus	Species	Aspergillaceae	Eukaryota	n.a.	latex	n.a.	PMID[21854017]
NPO12761	Rheum hotaoense	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7322	Plagiochila acanthophylla	Species	Plagiochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11673	Koelreuteria paniculata	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9015	Solanum arundo	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO395	Teucrium pilosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15212.1	Fraxinus chinensis subsp. rhynchophylla	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12761	Rheum hotaoense	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3313	Crotalaria trichotoma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11673	Koelreuteria paniculata	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11673	Koelreuteria paniculata	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15212.1	Fraxinus chinensis subsp. rhynchophylla	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9461	Gmelina leichhardtii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9015	Solanum arundo	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4454	Maytenus salicifolia	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5310	Eucalyptus bakeri	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3670	Crotalaria podocarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11673	Koelreuteria paniculata	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO737	Aspergillus japonicus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7322	Plagiochila acanthophylla	Species	Plagiochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8403	Annona coriacea	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4919	Kalanchoe daigremontiana	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11540	Acacia leptostachya	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO395	Teucrium pilosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3313	Crotalaria trichotoma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17461	Hedera canariensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13095	Pachycereus tehuantepecanus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10101	Rothmannia macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12761	Rheum hotaoense	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15212.1	Fraxinus chinensis subsp. rhynchophylla	Subspecies	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12045	Schottera nicaeensis	Species	Phyllophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9887	Protohermes grandis	Species	Corydalidae	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 NPC207057 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	154
0.1-0.2	1367
0.2-0.3	7998
0.3-0.4	15432
0.4-0.5	6900
0.5-0.6	5521
0.6-0.7	3864
0.7-0.8	1081
0.8-0.85	207
0.85-0.9	90
0.9-0.95	48
0.95-1	35

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 NPC207057 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	161
0.1-0.2	1632
0.2-0.3	4499
0.3-0.4	1999
0.4-0.5	431
0.5-0.6	175
0.6-0.7	145
0.7-0.8	74
0.8-0.85	15
0.85-0.9	16
0.9-0.95	1
0.95-1	2

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