NPASS Compound

Structure

NPC250218 OpenBabel06302215102D 32 36 0 0 1 0 0 0 0 0999 V2000 -1.7166 -1.1460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0181 -2.0747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9731 -2.2779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3646 -2.8001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6660 -3.7288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4096 -2.5968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1081 -1.6681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8469 -1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5004 -2.1903 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8466 -0.4885 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6918 0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6915 0.9773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9768 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8469 1.4652 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8472 2.4426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6938 2.9311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5401 2.4421 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3861 2.9306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3864 3.9306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2522 3.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2319 2.4417 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2316 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3856 0.9758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5398 1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5396 0.4873 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6932 0.9763 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6930 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8463 -0.4889 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 -5.0981 2.9413 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 2 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 6 0 0 0 10 8 1 6 0 0 0 10 11 1 0 0 0 0 10 30 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 30 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 6 0 0 0 15 27 1 0 0 0 0 16 17 1 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 25 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 22 23 1 0 0 0 0 22 32 1 6 0 0 0 23 24 1 0 0 0 0 25 24 1 1 0 0 0 25 27 1 0 0 0 0 25 26 1 0 0 0 0 27 26 1 6 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	440.4
Volume:	508.103
LogP:	7.626
LogD:	6.041
LogS:	-6.392
# Rotatable Bonds:	5
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.425
Synthetic Accessibility Score:	5.447
Fsp3:	0.935
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:	-5.13
MDCK Permeability:	1.1723762327164877e-05
Pgp-inhibitor:	0.006
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.976
30% Bioavailability (F30%):	0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	96.36444091796875%
Volume Distribution (VD):	1.224
Pgp-substrate:	1.8912508487701416%

ADMET: Metabolism

CYP1A2-inhibitor:	0.032
CYP1A2-substrate:	0.385
CYP2C19-inhibitor:	0.087
CYP2C19-substrate:	0.961
CYP2C9-inhibitor:	0.188
CYP2C9-substrate:	0.413
CYP2D6-inhibitor:	0.121
CYP2D6-substrate:	0.711
CYP3A4-inhibitor:	0.771
CYP3A4-substrate:	0.759

ADMET: Excretion

Clearance (CL):	7.141
Half-life (T1/2):	0.066

ADMET: Toxicity

hERG Blockers:	0.183
Human Hepatotoxicity (H-HT):	0.11
Drug-inuced Liver Injury (DILI):	0.049
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.244
Maximum Recommended Daily Dose:	0.894
Skin Sensitization:	0.807
Carcinogencity:	0.031
Eye Corrosion:	0.306
Eye Irritation:	0.283
Respiratory Toxicity:	0.558

Download Data

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

Natural Product: NPC250218

Natural Product ID:	NPC250218
*Common Name:**	BDHQMRXFDYJGII-IARBFMIJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BDHQMRXFDYJGII-IARBFMIJSA-N
Standard InCHI:	InChI=1S/C31H52O/c1-20(2)21(3)9-10-22(4)23-13-15-29(8)25-12-11-24-27(5,6)26(32)14-16-30(24)19-31(25,30)18-17-28(23,29)7/h20,22-26,32H,3,9-19H2,1-2,4-8H3/t22-,23-,24+,25-,26+,28-,29+,30-,31+/m1/s1
SMILES:	CC(C)C(=C)CC[C@@H](C)[C@H]1CC[C@@]2(C)[C@H]3CC[C@H]4C(C)(C)[C@H](CC[C@]54C[C@@]35CC[C@]12C)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: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
NPO15351	Streptomyces prunicolor	Species	Streptomycetaceae	Bacteria	n.a.	mycelium	n.a.	DOI[10.1021/np50098a008]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	roots	n.a.	n.a.	PMID[12444706]
NPO11898	Lobophora variegata	Species	Dictyotaceae	Eukaryota	n.a.	at depths of 630 m at El Mdano (Tenerife, Canary Islands)	n.a.	PMID[26126835]
NPO5247	Elaphoglossum lindbergii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26689830]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12853	Leucocarpus perfoliatus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12633	Rapanea neurophylla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11206	Trifolium hybridum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12853	Leucocarpus perfoliatus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12633	Rapanea neurophylla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12853	Leucocarpus perfoliatus	Species	Phrymaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1044	Caiman crocodilus	Species	Alligatoridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10530	Aconitum subcuneatum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11898	Lobophora variegata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1116	Periconia atropurpurea	Species	Periconiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11527	Ibacus peronii	Species	Scyllaridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5714	Rogeria adenophylla	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15351	Streptomyces prunicolor	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5247	Elaphoglossum lindbergii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12633	Rapanea neurophylla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2996	Pistacia atlantica	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9363	Ferula ammoniacum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7560	Tachardia acaciae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6541	Scrophularia buergeriana	Species	Scrophulariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9606	Castanea dentata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2207	Sphaerella rubella	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11206	Trifolium hybridum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12146	Stemodia maritima	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23883	Penicillium abidjanum	Species	Aspergillaceae	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 NPC250218 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	184
0.1-0.2	2489
0.2-0.3	13754
0.3-0.4	11929
0.4-0.5	5134
0.5-0.6	5315
0.6-0.7	2848
0.7-0.8	840
0.8-0.85	116
0.85-0.9	67
0.9-0.95	10
0.95-1	11

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 NPC250218 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	198
0.1-0.2	2748
0.2-0.3	4377
0.3-0.4	1263
0.4-0.5	218
0.5-0.6	158
0.6-0.7	147
0.7-0.8	38
0.8-0.85	2
0.85-0.9	1
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