NPASS Compound

Structure

NPC141862 OpenBabel06302216022D 45 49 0 0 1 0 0 0 0 0999 V2000 2.5363 -2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5363 -1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3817 -0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2271 -1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2271 -2.4405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3817 -2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3817 -3.9048 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0725 -2.9286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0725 -0.9762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 -0.9762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6908 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8454 -1.4643 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8454 -1.4643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6908 -0.9762 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6908 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8454 0.4881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0659 1.0498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5083 1.4603 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0849 1.6382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0119 2.6117 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6816 1.5482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7267 2.1500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2704 2.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7690 2.0719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7239 1.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1802 1.2083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4819 0.6857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5270 0.0839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3066 -0.4778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8191 -0.2865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6648 0.2139 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9598 0.6466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4716 1.4920 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6995 0.3594 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3879 -1.6145 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8642 -0.8883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3523 -1.7337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2876 -1.0662 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5305 0.9202 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6485 2.4955 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3434 3.3853 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 -2.5363 0.4881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8454 -2.4405 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 2 10 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 43 1 0 0 0 0 14 15 1 0 0 0 0 14 45 1 6 0 0 0 15 16 1 0 0 0 0 15 39 1 1 0 0 0 16 17 1 0 0 0 0 16 44 1 6 0 0 0 17 18 1 1 0 0 0 17 43 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 24 25 1 0 0 0 0 24 42 1 0 0 0 0 25 26 2 0 0 0 0 25 41 1 0 0 0 0 26 27 1 0 0 0 0 26 40 1 0 0 0 0 27 28 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 30 37 1 0 0 0 0 31 32 2 0 0 0 0 31 36 1 0 0 0 0 32 33 1 0 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	634.08
Volume:	559.352
LogP:	1.385
LogD:	0.335
LogS:	-1.885
# Rotatable Bonds:	3
TPSA:	310.66
# H-Bond Aceptor:	18
# H-Bond Donor:	11
# Rings:	5
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.098
Synthetic Accessibility Score:	6.186
Fsp3:	0.222
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.948
MDCK Permeability:	8.492809683957603e-06
Pgp-inhibitor:	0.09
Pgp-substrate:	0.019
Human Intestinal Absorption (HIA):	0.986
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.004
Plasma Protein Binding (PPB):	90.80982208251953%
Volume Distribution (VD):	0.558
Pgp-substrate:	24.731168746948242%

ADMET: Metabolism

CYP1A2-inhibitor:	0.154
CYP1A2-substrate:	0.007
CYP2C19-inhibitor:	0.014
CYP2C19-substrate:	0.027
CYP2C9-inhibitor:	0.428
CYP2C9-substrate:	0.033
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.022
CYP3A4-substrate:	0.002

ADMET: Excretion

Clearance (CL):	7.501
Half-life (T1/2):	0.952

ADMET: Toxicity

hERG Blockers:	0.192
Human Hepatotoxicity (H-HT):	0.14
Drug-inuced Liver Injury (DILI):	0.973
AMES Toxicity:	0.161
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.005
Skin Sensitization:	0.95
Carcinogencity:	0.015
Eye Corrosion:	0.003
Eye Irritation:	0.905
Respiratory Toxicity:	0.004

Download Data

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

Natural Product: NPC141862

Natural Product ID:	NPC141862
*Common Name:**	WUVWCJIFVJNNKM-LNBIJUBGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WUVWCJIFVJNNKM-LNBIJUBGSA-N
Standard InCHI:	InChI=1S/C27H22O18/c28-10-1-6(2-11(29)17(10)33)24(39)45-27-22(38)23-19(35)13(43-27)5-42-25(40)8-4-12(30)18(34)20(36)14(8)7-3-9(26(41)44-23)16(32)21(37)15(7)31/h1-4,13,19,22-23,27-38H,5H2/t13-,19-,22-,23+,27-/m1/s1
SMILES:	c1c(cc(c(c1O)O)O)C(=O)O[C@@H]1[C@@H]([C@@H]2[C@@H]([C@@H](COC(=O)c3cc(c(c(c3-c3cc(c(c(c3O)O)O)C(=O)O2)O)O)O)O1)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:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[17637068]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18302336]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22432912]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	root	n.a.	PMID[26724423]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	stem	n.a.	PMID[26724423]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23772	Tetradium glabrifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1759	Alexandrium excavatum	Species	Gonyaulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15329	Rhizoplaca baranowii	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13647	Calcarisporium thermophilum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1109	Corydalis persica	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2330	Alchornea cordifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13278	Strychnos spinosa	Species	Loganiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14947	Lathyrus tingitanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6906	Atalantia wightii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3761	Plectosphaerella cucumerina	Species	Plectosphaerellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18873.2	Salmonella enterica subsp. enterica serovar bovismorbificans	Subspecies	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO23772	Tetradium glabrifolium	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15145	Rauvolfia salicifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3965	Corynanthe pachyceras	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15233	Balanophora japonica	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14526	Plectranthus caninus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13848	Amomum daniellii	Species	Zingiberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5470	Cynoglossum amabile	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5398	Peucedanum oroselinum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12487	Juniperus horizontalis	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7521	Hygrophorus eburneus	Species	Hygrophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16801	Cota tinctoria	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11430	Inula grantioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10098	Glycosmis pseudoracemosa	Species	Rutaceae	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 NPC141862 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	407
0.1-0.2	1636
0.2-0.3	3476
0.3-0.4	7918
0.4-0.5	9508
0.5-0.6	5605
0.6-0.7	5642
0.7-0.8	6627
0.8-0.85	1424
0.85-0.9	398
0.9-0.95	52
0.95-1	4

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 NPC141862 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	359
0.1-0.2	921
0.2-0.3	1863
0.3-0.4	2761
0.4-0.5	1851
0.5-0.6	976
0.6-0.7	276
0.7-0.8	116
0.8-0.85	26
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