NPASS Compound

Structure

NPC32710 OpenBabel06302215312D 30 33 0 0 1 0 0 0 0 0999 V2000 -0.0015 1.9519 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8463 1.4638 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6914 1.9514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6917 2.9271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5368 3.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5371 4.3904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3816 2.9266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8692 2.0815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8935 2.0818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2267 3.4142 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 2 1 1 1 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 11 2 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:	574.35
Volume:	596.318
LogP:	3.25
LogD:	2.919
LogS:	-4.241
# Rotatable Bonds:	6
TPSA:	122.52
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.333
Synthetic Accessibility Score:	5.654
Fsp3:	0.818
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:	-5.119
MDCK Permeability:	1.263890226255171e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.636
Human Intestinal Absorption (HIA):	0.007
20% Bioavailability (F20%):	0.019
30% Bioavailability (F30%):	0.119

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.11
Plasma Protein Binding (PPB):	80.2900619506836%
Volume Distribution (VD):	1.91
Pgp-substrate:	15.194355010986328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.12
CYP2C19-inhibitor:	0.007
CYP2C19-substrate:	0.584
CYP2C9-inhibitor:	0.032
CYP2C9-substrate:	0.026
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.023
CYP3A4-inhibitor:	0.765
CYP3A4-substrate:	0.572

ADMET: Excretion

Clearance (CL):	1.871
Half-life (T1/2):	0.282

ADMET: Toxicity

hERG Blockers:	0.038
Human Hepatotoxicity (H-HT):	0.323
Drug-inuced Liver Injury (DILI):	0.171
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.879
Maximum Recommended Daily Dose:	0.752
Skin Sensitization:	0.713
Carcinogencity:	0.085
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.976

Download Data

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

Natural Product: NPC32710

Natural Product ID:	NPC32710
*Common Name:**	QXDHYSHOINNEAZ-HSIBUNQISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	QXDHYSHOINNEAZ-HSIBUNQISA-N
Standard InCHI:	InChI=1S/C29H48O/c1-19(8-9-20(2)27(3,4)5)24-12-13-25-23-11-10-21-18-22(30)14-16-28(21,6)26(23)15-17-29(24,25)7/h10,19,22-26,30H,2,8-9,11-18H2,1,3-7H3/t19-,22+,23+,24-,25+,26+,28+,29-/m1/s1
SMILES:	C[C@H](CCC(=C)C(C)(C)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:	5283645
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]
NPO17794	Streptomyces violaceusniger	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[8557611]
NPO4002	Lappula intermedia	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11673	Koelreuteria paniculata	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
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]
NPO18560	Tripterospermum japonicum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7322	Plagiochila acanthophylla	Species	Plagiochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12761	Rheum hotaoense	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11673	Koelreuteria paniculata	Species	Sapindaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3313	Crotalaria trichotoma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18560	Tripterospermum japonicum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4002	Lappula intermedia	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
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]
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[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]
NPO5310	Eucalyptus bakeri	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9811	Macrotyloma uniflorum	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]
NPO17461	Hedera canariensis	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19809	Streptomyces roseoviolaceus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18560	Tripterospermum japonicum	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7322	Plagiochila acanthophylla	Species	Plagiochilaceae	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]
NPO9887	Protohermes grandis	Species	Corydalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11228	Fritillaria pallidiflora	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9461	Gmelina leichhardtii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4454	Maytenus salicifolia	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4919	Kalanchoe daigremontiana	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19587	Cordia rothii	Species	Cordiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3670	Crotalaria podocarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11540	Acacia leptostachya	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO737	Aspergillus japonicus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3313	Crotalaria trichotoma	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8403	Annona coriacea	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13095	Pachycereus tehuantepecanus	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19260	Zanthoxylum petiolare	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10101	Rothmannia macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17794	Streptomyces violaceusniger	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9015	Solanum arundo	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12761	Rheum hotaoense	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14323	Bossiella orbigniana	Species	Corallinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12045	Schottera nicaeensis	Species	Phyllophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12920	Erimacrus isenbeckii	Species	Atelecyclidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO395	Teucrium pilosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4002	Lappula intermedia	Species	Boraginaceae	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 NPC32710 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 NPC32710 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