NPASS Compound

Structure

NPC87781 OpenBabel06302216012D 39 42 0 0 1 0 0 0 0 0999 V2000 5.8545 -1.2044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8327 -0.9965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1417 -0.0454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1198 0.1625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4289 1.1136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4070 1.3215 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7597 1.8567 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7890 -0.5806 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.4800 -1.5317 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.5018 -1.7396 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1491 -2.2748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8401 -3.2259 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.1272 -2.0669 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1854 -0.4612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 -0.6691 0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8060 -1.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8005 -1.5827 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3005 -2.4487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3005 -2.4487 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8005 -3.3147 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 C 0 0 1 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 1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 1 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 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 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 2 3 0 0 0 1 14 1 0 0 0 0 2 10 1 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 8 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 11 1 1 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 14 15 2 3 0 0 0 15 23 1 0 0 0 0 15 16 1 0 0 0 0 16 21 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 39 1 0 0 0 0 19 20 2 0 0 0 0 19 27 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 28 27 1 6 0 0 0 28 29 1 0 0 0 0 28 35 1 0 0 0 0 29 30 1 0 0 0 0 29 38 1 1 0 0 0 30 31 1 0 0 0 0 30 37 1 6 0 0 0 31 32 1 0 0 0 0 31 36 1 1 0 0 0 32 33 1 6 0 0 0 32 35 1 0 0 0 0 33 34 1 0 0 0 0 M CHG 2 15 1 39 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	562.32
Volume:	556.239
LogP:	3.512
LogD:	3.58
LogS:	-3.281
# Rotatable Bonds:	9
TPSA:	153.75
# H-Bond Aceptor:	9
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.285
Synthetic Accessibility Score:	5.375
Fsp3:	1.0
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.039
MDCK Permeability:	3.317778100608848e-05
Pgp-inhibitor:	0.039
Pgp-substrate:	0.176
Human Intestinal Absorption (HIA):	0.033
20% Bioavailability (F20%):	0.077
30% Bioavailability (F30%):	0.617

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.016
Plasma Protein Binding (PPB):	91.46843719482422%
Volume Distribution (VD):	0.932
Pgp-substrate:	3.0855302810668945%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.146
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.825
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.178
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.083
CYP3A4-inhibitor:	0.024
CYP3A4-substrate:	0.06

ADMET: Excretion

Clearance (CL):	5.099
Half-life (T1/2):	0.242

ADMET: Toxicity

hERG Blockers:	0.303
Human Hepatotoxicity (H-HT):	0.7
Drug-inuced Liver Injury (DILI):	0.906
AMES Toxicity:	0.551
Rat Oral Acute Toxicity:	0.2
Maximum Recommended Daily Dose:	0.803
Skin Sensitization:	0.959
Carcinogencity:	0.581
Eye Corrosion:	0.08
Eye Irritation:	0.196
Respiratory Toxicity:	0.969

Download Data

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

Natural Product: NPC87781

Natural Product ID:	NPC87781
*Common Name:**	DHHFDKNIEVKVKS-RYGANQNKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DHHFDKNIEVKVKS-RYGANQNKSA-N
Standard InCHI:	InChI=1S/C24H26N2O13/c27-8-17-18(29)19(30)20(31)24(39-17)38-16-6-10-5-14(23(36)37)26(13(10)7-15(16)28)2-1-9-3-11(21(32)33)25-12(4-9)22(34)35/h1-3,6-7,12,14,17-20,24,27,29-31H,4-5,8H2,(H4,28,32,33,34,35,36,37)/t12-,14+,17-,18-,19+,20-,24-/m1/s1
SMILES:	C(=C1C=C(C(=O)O)N[C@H](C1)C(=O)O)C=[N+]1c2cc(c(cc2C[C@H]1C(=O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)[O-]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6325438
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001435] Betalains [CHEMONTID:0001434] Betacyanins 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
NPO4302	Stylocheilus longicauda	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10924193]
NPO4302	Stylocheilus longicauda	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11076568]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12880321]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	bark	n.a.	PMID[22708987]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22708987]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2614422]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26562741]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	Aerial Parts	n.a.	n.a.	PMID[29122483]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29517238]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31625751]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	Along the Valencian coast, Spain	2020-Jun&Jul	PMID[35161358]
NPO4302	Stylocheilus longicauda	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[4833645]
NPO1653	Streptomyces longissimus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[903851]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	Herb	n.a.	n.a.	Database[FooDB]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO4080	Salix purpurea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7507	Portulaca grandiflora	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5525	Mesembryanthemum edule	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8240	Opuntia vulgaris	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO118	Ustilago maydis	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1034	Ophiorrhiza liukiuensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4080	Salix purpurea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5525	Mesembryanthemum edule	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7507	Portulaca grandiflora	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8240	Opuntia vulgaris	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1034	Ophiorrhiza liukiuensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO118	Ustilago maydis	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4080	Salix purpurea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6545	Artemisia sieversiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4640	Portulaca oleracea	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1653	Streptomyces longissimus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4080	Salix purpurea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9978	Indigofera microcarpa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2644	Portulaca pilosa	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9332	Corydalis longipes	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8775	Streptomyces rubellomurinus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4302	Stylocheilus longicauda	Species	Aplysiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12980	Acronychia pedunculata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10583	Streptomyces echinatus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO6048	Sarcodictyon roseum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7271	Stachys affinis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4506	Corydalis paniculigera	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7507	Portulaca grandiflora	Species	Portulacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2178	Cachrys trifida	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1034	Ophiorrhiza liukiuensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5427	Sabal peregrina	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15839	Nicotiana repanda	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO118	Ustilago maydis	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8240	Opuntia vulgaris	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6545	Artemisia sieversiana	Species	Asteraceae	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 NPC87781 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	352
0.1-0.2	1710
0.2-0.3	7177
0.3-0.4	10535
0.4-0.5	10215
0.5-0.6	10812
0.6-0.7	1773
0.7-0.8	107
0.8-0.85	10
0.85-0.9	6
0.9-0.95	0
0.95-1	0

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 NPC87781 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	192
0.1-0.2	536
0.2-0.3	945
0.3-0.4	1958
0.4-0.5	2716
0.5-0.6	2220
0.6-0.7	573
0.7-0.8	10
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