NPASS Compound

Structure

NPC129391 OpenBabel06302215222D 51 59 0 0 1 0 0 0 0 0999 V2000 3.6512 0.8663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5896 0.5769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8082 -0.3806 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0882 -1.0486 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1498 -0.7591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9312 0.1983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9927 0.4878 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8737 1.2775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5653 1.6768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5653 2.4754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8737 2.8746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1821 2.4754 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1821 1.6768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4388 1.3850 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1691 1.2468 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 0.6327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3289 0.6883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6514 1.3579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2327 1.9720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4915 1.9165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3851 3.5394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6308 1.4313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4496 -0.0976 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8355 -0.5163 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8061 -1.4979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0588 -1.9633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8942 -1.4471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8648 -0.4654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5747 0.2133 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5410 0.0379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8723 -0.8866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8386 -1.0620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4737 -0.3128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1424 0.6118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1761 0.7871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7774 1.3609 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1699 -1.9865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1486 1.0982 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6140 1.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5956 1.9924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0610 2.8572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5447 3.6927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5631 3.6633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0977 2.7985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0101 4.5575 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1754 0.9663 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7591 -1.9124 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6415 -2.0142 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4158 2.9664 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7466 -0.6701 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 51 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 23 1 0 0 0 0 8 13 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 50 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 14 13 1 1 0 0 0 14 15 1 0 0 0 0 14 46 1 0 0 0 0 15 20 2 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 18 19 2 0 0 0 0 18 22 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 23 16 1 6 0 0 0 23 24 1 0 0 0 0 24 47 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 49 1 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 48 1 0 0 0 0 28 47 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 1 0 0 0 29 38 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 32 37 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 34 36 1 0 0 0 0 38 39 1 6 0 0 0 38 46 1 0 0 0 0 39 44 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 42 45 1 0 0 0 0 43 44 1 0 0 0 0 46 47 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	680.2
Volume:	689.635
LogP:	6.467
LogD:	3.767
LogS:	-4.522
# Rotatable Bonds:	3
TPSA:	182.07
# H-Bond Aceptor:	9
# H-Bond Donor:	9
# Rings:	9
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.092
Synthetic Accessibility Score:	5.329
Fsp3:	0.143
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.415
MDCK Permeability:	5.558961674978491e-06
Pgp-inhibitor:	0.518
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.995
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	95.97649383544922%
Volume Distribution (VD):	0.263
Pgp-substrate:	7.02674674987793%

ADMET: Metabolism

CYP1A2-inhibitor:	0.127
CYP1A2-substrate:	0.838
CYP2C19-inhibitor:	0.954
CYP2C19-substrate:	0.049
CYP2C9-inhibitor:	0.753
CYP2C9-substrate:	0.999
CYP2D6-inhibitor:	0.139
CYP2D6-substrate:	0.401
CYP3A4-inhibitor:	0.195
CYP3A4-substrate:	0.654

ADMET: Excretion

Clearance (CL):	7.124
Half-life (T1/2):	0.548

ADMET: Toxicity

hERG Blockers:	0.137
Human Hepatotoxicity (H-HT):	0.087
Drug-inuced Liver Injury (DILI):	0.379
AMES Toxicity:	0.2
Rat Oral Acute Toxicity:	0.832
Maximum Recommended Daily Dose:	0.998
Skin Sensitization:	0.941
Carcinogencity:	0.009
Eye Corrosion:	0.003
Eye Irritation:	0.901
Respiratory Toxicity:	0.029

Download Data

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

Natural Product: NPC129391

Natural Product ID:	NPC129391
*Common Name:**	FWPQMKZSFDFHKZ-CVVULUIWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FWPQMKZSFDFHKZ-CVVULUIWSA-N
Standard InCHI:	InChI=1S/C42H32O9/c43-21-5-1-18(2-6-21)33-28-14-23(45)9-10-27(28)37-36-29(15-26(48)16-30(36)49)38(33)40-32(51)17-31(50)39-35(20-11-24(46)13-25(47)12-20)34(41(37)42(39)40)19-3-7-22(44)8-4-19/h1-17,33-35,37-38,41,43-51H/t33-,34+,35+,37+,38+,41-/m1/s1
SMILES:	c1cc(ccc1[C@@H]1c2cc(ccc2[C@H]2c3c(cc(cc3O)O)[C@@H]1c1c(cc(c3[C@@H](c4cc(cc(c4)O)O)[C@H](c4ccc(cc4)O)[C@H]2c13)O)O)O)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:0002650] Diarylheptanoids [CHEMONTID:0002651] Linear diarylheptanoids

*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
NPO5650	Eupatorium glutinosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12027751]
NPO1782	Piper caninum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15270572]
NPO98	Leucosceptrum canum	Species	Lamiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[15524427]
NPO6522	Polyalthia evecta	Species	Annonaceae	Eukaryota	roots	n.a.	n.a.	PMID[16441071]
NPO6522	Polyalthia evecta	Species	Annonaceae	Eukaryota	n.a.	root	n.a.	PMID[16441071]
NPO9804	Cinnamosma macrocarpa	Species	Canellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17286431]
NPO25661	Vatica rassak	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11541	Curcuma xanthorrhiza	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2042	Garcinia bancana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10915	Heliotropium hirsutum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11541	Curcuma xanthorrhiza	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25661	Vatica rassak	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10915	Heliotropium hirsutum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2042	Garcinia bancana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2042	Garcinia bancana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1782	Piper caninum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5650	Eupatorium glutinosum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14958	Duguetia eximia	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15640	Sideritis chamaedryfolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17995	Xeromphis spinosa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13778	Melandrium turkestanicum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO6522	Polyalthia evecta	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9406	Cotula filicula	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16805	Senecio cisplatinus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14697	Ustilago esculenta	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25661	Vatica rassak	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11736	Bulla striata	Species	Bullidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9804	Cinnamosma macrocarpa	Species	Canellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14439	Marasmius oreades	Species	Marasmiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13334	Senecio toluccanus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14476	Sterculia alata	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11541	Curcuma xanthorrhiza	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO98	Leucosceptrum canum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16691	Viguiera radula	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11202	Maytenus imbricata	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10915	Heliotropium hirsutum	Species	Heliotropiaceae	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 NPC129391 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	515
0.1-0.2	1988
0.2-0.3	5198
0.3-0.4	13168
0.4-0.5	5855
0.5-0.6	8163
0.6-0.7	6581
0.7-0.8	1102
0.8-0.85	106
0.85-0.9	15
0.9-0.95	5
0.95-1	1

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 NPC129391 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	445
0.1-0.2	1024
0.2-0.3	1451
0.3-0.4	3263
0.4-0.5	1736
0.5-0.6	964
0.6-0.7	238
0.7-0.8	29
0.8-0.85	0
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