NPASS Compound

Structure

NPC44001 OpenBabel06302215182D 45 49 0 0 1 0 0 0 0 0999 V2000 0.6801 -5.0098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6801 -5.0098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1801 -4.1438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6801 -3.2778 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1801 -2.4118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6801 -1.5457 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8141 -2.0457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1801 -0.6797 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5869 0.2338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8437 0.9030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0223 0.4030 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6101 1.2120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1856 -0.5752 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5575 -1.2443 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5086 -0.9353 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7165 0.0428 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6676 0.3519 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4596 -0.6263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4107 -0.3173 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3618 -0.0083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5697 0.9699 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8265 1.6390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4957 2.3822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5175 2.5901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8755 1.3300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1323 1.9991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1813 1.6901 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9734 0.7120 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2302 1.3811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4381 2.3593 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5207 1.2789 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3496 -2.2225 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5462 -1.0457 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5462 -0.0457 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4122 0.4543 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4122 1.4543 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5462 1.9543 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6801 1.4543 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8141 1.9543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8141 2.9543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6801 0.4543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5462 2.9543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2782 1.9543 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2782 -0.0457 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1801 -5.8759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 45 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 33 1 0 0 0 0 8 6 1 6 0 0 0 8 9 1 0 0 0 0 8 13 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 28 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 32 1 6 0 0 0 16 15 1 6 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 25 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 31 1 6 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 22 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 27 30 1 6 0 0 0 28 29 1 6 0 0 0 34 33 1 6 0 0 0 34 35 1 0 0 0 0 34 41 1 0 0 0 0 35 36 1 0 0 0 0 35 44 1 1 0 0 0 36 37 1 0 0 0 0 36 43 1 6 0 0 0 37 38 1 0 0 0 0 37 42 1 1 0 0 0 38 39 1 6 0 0 0 38 41 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	636.42
Volume:	662.269
LogP:	3.133
LogD:	2.966
LogS:	-4.108
# Rotatable Bonds:	7
TPSA:	160.07
# H-Bond Aceptor:	9
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.208
Synthetic Accessibility Score:	5.743
Fsp3:	0.889
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:	-5.122
MDCK Permeability:	8.927225280785933e-06
Pgp-inhibitor:	0.999
Pgp-substrate:	0.406
Human Intestinal Absorption (HIA):	0.653
20% Bioavailability (F20%):	0.704
30% Bioavailability (F30%):	0.227

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.048
Plasma Protein Binding (PPB):	80.1131820678711%
Volume Distribution (VD):	0.676
Pgp-substrate:	7.391542434692383%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.185
CYP2C19-inhibitor:	0.004
CYP2C19-substrate:	0.641
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.065
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.074
CYP3A4-substrate:	0.106

ADMET: Excretion

Clearance (CL):	1.602
Half-life (T1/2):	0.463

ADMET: Toxicity

hERG Blockers:	0.092
Human Hepatotoxicity (H-HT):	0.375
Drug-inuced Liver Injury (DILI):	0.018
AMES Toxicity:	0.05
Rat Oral Acute Toxicity:	0.827
Maximum Recommended Daily Dose:	0.97
Skin Sensitization:	0.551
Carcinogencity:	0.049
Eye Corrosion:	0.003
Eye Irritation:	0.015
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC44001

Natural Product ID:	NPC44001
*Common Name:**	ARPGURKWJGBPTN-ASPSLOFTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ARPGURKWJGBPTN-ASPSLOFTSA-N
Standard InCHI:	InChI=1S/C36H60O9/c1-19(2)10-9-13-35(7,45-31-30(43)29(42)28(41)22(18-37)44-31)20-11-15-34(6)27(20)21(38)16-24-33(5)14-12-25(39)32(3,4)23(33)17-26(40)36(24,34)8/h10,17,20-22,24-31,37-43H,9,11-16,18H2,1-8H3/t20-,21+,22+,24+,25-,26-,27+,28+,29-,30+,31-,33-,34+,35-,36-/m0/s1
SMILES:	CC(=CCC[C@@](C)([C@H]1CC[C@]2(C)[C@H]1[C@@H](C[C@@H]1[C@@]3(C)CC[C@@H](C(C)(C)C3=C[C@@H]([C@@]21C)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)C
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:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0001580] Triterpene glycosides [CHEMONTID:0002358] Triterpene saponins

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO10540	Passiflora incarnata	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2026709]
NPO11248	Tachigalia paniculata	n.a.	n.a.	n.a.	leaves	n.a.	n.a.	PMID[12444671]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11000019]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075755]
NPO21854	Pterocladiella tenuis	Species	Gelidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18805	Tripolium pannonicum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO210	Uvaria calamistrata	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14255	Streptomyces flocculus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19635	Coreopsis nodosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7998	Senecio paludaffinis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC44001 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	238
0.1-0.2	1698
0.2-0.3	5058
0.3-0.4	11653
0.4-0.5	10193
0.5-0.6	6079
0.6-0.7	4600
0.7-0.8	2439
0.8-0.85	518
0.85-0.9	167
0.9-0.95	46
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
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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 NPC44001 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	191
0.1-0.2	1870
0.2-0.3	4104
0.3-0.4	1947
0.4-0.5	583
0.5-0.6	246
0.6-0.7	171
0.7-0.8	27
0.8-0.85	11
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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