NPASS Compound

Structure

NPC184610 OpenBabel06302215562D 40 43 0 0 1 0 0 0 0 0999 V2000 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8614 1.5906 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1953 2.0945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6888 2.4438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2708 3.3523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2751 2.5913 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8751 2.5170 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1782 3.4700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4077 2.2310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8010 1.7719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0020 1.2017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9834 0.5974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7477 0.0407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3340 -0.1068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4995 -0.6883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0786 -1.1223 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3523 -2.0841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4923 -0.9749 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3268 -0.3934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7776 -0.6461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0215 -1.6159 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1742 -0.6833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4693 -0.9322 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2135 3.5894 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 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 0.0000 -3.0000 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 3 4 1 6 0 0 0 5 3 1 1 0 0 0 5 6 1 0 0 0 0 5 39 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 40 1 6 0 0 0 10 9 1 6 0 0 0 10 38 1 0 0 0 0 10 11 1 0 0 0 0 10 39 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 35 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 38 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 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 19 37 1 1 0 0 0 20 21 1 1 0 0 0 20 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 26 32 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 36 1 0 0 0 0 29 30 1 0 0 0 0 29 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	554.32
Volume:	588.175
LogP:	4.908
LogD:	4.394
LogS:	-4.963
# Rotatable Bonds:	2
TPSA:	105.45
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.311
Synthetic Accessibility Score:	6.749
Fsp3:	0.606
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:	-4.72
MDCK Permeability:	3.301164906588383e-05
Pgp-inhibitor:	0.298
Pgp-substrate:	0.991
Human Intestinal Absorption (HIA):	0.018
20% Bioavailability (F20%):	0.024
30% Bioavailability (F30%):	0.963

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.101
Plasma Protein Binding (PPB):	97.76415252685547%
Volume Distribution (VD):	0.789
Pgp-substrate:	2.756302833557129%

ADMET: Metabolism

CYP1A2-inhibitor:	0.066
CYP1A2-substrate:	0.319
CYP2C19-inhibitor:	0.23
CYP2C19-substrate:	0.801
CYP2C9-inhibitor:	0.585
CYP2C9-substrate:	0.937
CYP2D6-inhibitor:	0.137
CYP2D6-substrate:	0.823
CYP3A4-inhibitor:	0.894
CYP3A4-substrate:	0.673

ADMET: Excretion

Clearance (CL):	12.877
Half-life (T1/2):	0.049

ADMET: Toxicity

hERG Blockers:	0.537
Human Hepatotoxicity (H-HT):	0.952
Drug-inuced Liver Injury (DILI):	0.958
AMES Toxicity:	0.307
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.997
Skin Sensitization:	0.927
Carcinogencity:	0.82
Eye Corrosion:	0.003
Eye Irritation:	0.025
Respiratory Toxicity:	0.961

Download Data

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

Natural Product: NPC184610

Natural Product ID:	NPC184610
*Common Name:**	JFIXFPOXRZPCCA-CFQHKURLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JFIXFPOXRZPCCA-CFQHKURLSA-N
Standard InCHI:	InChI=1S/C33H46O7/c1-7-19(2)31-23(6)29(35)18-33(40-31)17-26-16-25(39-33)13-12-21(4)30(36)20(3)10-8-9-11-24-15-28(34)22(5)14-27(24)32(37)38-26/h8-12,14-15,19-20,23,25-26,29-31,34-36H,7,13,16-18H2,1-6H3/b10-8+,11-9+,21-12+/t19-,20-,23-,25+,26-,29-,30-,31+,33-/m0/s1
SMILES:	CC[C@H](C)[C@@H]1[C@@H](C)[C@H](C[C@]2(C[C@@H]3C[C@@H](C/C=C(C)/[C@H]([C@@H](C)/C=C/C=C/c4cc(c(C)cc4C(=O)O3)O)O)O2)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000147] Macrolides and analogues [CHEMONTID:0002902] Milbemycins

*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
NPO2303	Sinularia scabra	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12502336]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1367520]
NPO2303	Sinularia scabra	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[15620256]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974609]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21381678]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21667925]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22118684]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	roots and rhizomes	n.a.	n.a.	PMID[25835537]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26692349]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33089690]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8626236]
NPO14368	Stephania sinica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11138	Veronicastrum sibiricum	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO350	Piper cenocladum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11138	Veronicastrum sibiricum	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO350	Piper cenocladum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14368	Stephania sinica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11138	Veronicastrum sibiricum	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28362	Tacca paxiana	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14368	Stephania sinica	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14993	Poecillastra laminaris	Species	Vulcanellidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2303	Sinularia scabra	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3282	Baeckea brevifolia	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13362	Scabiosa bipinnata	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15848	Veratrum nigrum	Species	Melanthiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16671	Lysimachia vulgaris	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13532	Prorocentrum hoffmannianum	Species	Prorocentraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14185	Helianthopsis utcubambensis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO350	Piper cenocladum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11138	Veronicastrum sibiricum	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15499	Boletus radicans	Species	Boletaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5000	Cordyceps brongniartii	Species	Cordycipitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10754	Zanthoxylum clava-herculis	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12115	Odontaster validus	Species	Odontasteridae	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 NPC184610 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	327
0.1-0.2	1267
0.2-0.3	2531
0.3-0.4	5279
0.4-0.5	9943
0.5-0.6	7914
0.6-0.7	7469
0.7-0.8	7505
0.8-0.85	412
0.85-0.9	45
0.9-0.95	3
0.95-1	2

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 NPC184610 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	273
0.1-0.2	831
0.2-0.3	1437
0.3-0.4	2473
0.4-0.5	2175
0.5-0.6	1288
0.6-0.7	515
0.7-0.8	154
0.8-0.85	4
0.85-0.9	0
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