NPASS Compound

Structure

NPC93956 OpenBabel06302215142D 27 30 0 0 1 0 0 0 0 0999 V2000 -2.5775 0.4810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7048 -0.0232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8318 0.4805 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8316 1.4412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0005 1.9213 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 0.0007 2.8826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8327 3.3628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6650 2.8822 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3294 2.8819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1619 3.3621 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9937 2.8816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9935 1.9203 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1615 1.4401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3292 1.9206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4972 1.4404 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6648 1.9210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8323 1.4408 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8321 0.4801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0003 -1.0079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8732 -1.5116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7459 -1.0074 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6189 -1.5111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8724 -1.5120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8722 -2.5199 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7454 -1.0083 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6181 -1.5125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 1 0 0 0 3 4 1 0 0 0 0 3 19 1 0 0 0 0 4 5 1 0 0 0 0 5 17 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 16 2 0 0 0 0 8 9 1 0 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 6 0 0 0 18 19 1 0 0 0 0 19 20 1 6 0 0 0 20 21 2 0 0 0 0 20 24 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	368.21
Volume:	387.388
LogP:	3.94
LogD:	3.8
LogS:	-4.096
# Rotatable Bonds:	5
TPSA:	54.56
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.506
Synthetic Accessibility Score:	3.859
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.849
MDCK Permeability:	2.277836210851092e-05
Pgp-inhibitor:	0.95
Pgp-substrate:	0.693
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.427
30% Bioavailability (F30%):	0.024

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.992
Plasma Protein Binding (PPB):	83.16973114013672%
Volume Distribution (VD):	1.79
Pgp-substrate:	7.559574604034424%

ADMET: Metabolism

CYP1A2-inhibitor:	0.906
CYP1A2-substrate:	0.948
CYP2C19-inhibitor:	0.849
CYP2C19-substrate:	0.87
CYP2C9-inhibitor:	0.612
CYP2C9-substrate:	0.221
CYP2D6-inhibitor:	0.956
CYP2D6-substrate:	0.856
CYP3A4-inhibitor:	0.879
CYP3A4-substrate:	0.907

ADMET: Excretion

Clearance (CL):	5.765
Half-life (T1/2):	0.415

ADMET: Toxicity

hERG Blockers:	0.954
Human Hepatotoxicity (H-HT):	0.742
Drug-inuced Liver Injury (DILI):	0.902
AMES Toxicity:	0.19
Rat Oral Acute Toxicity:	0.969
Maximum Recommended Daily Dose:	0.992
Skin Sensitization:	0.79
Carcinogencity:	0.943
Eye Corrosion:	0.005
Eye Irritation:	0.034
Respiratory Toxicity:	0.983

Download Data

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

Natural Product: NPC93956

Natural Product ID:	NPC93956
*Common Name:**	NMLUOJBSAYAYEM-XPOGPMDLSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NMLUOJBSAYAYEM-XPOGPMDLSA-N
Standard InCHI:	InChI=1S/C22H28N2O3/c1-4-14-12-24-10-9-16-15-7-5-6-8-19(15)23-21(16)20(24)11-17(14)18(13-26-2)22(25)27-3/h5-8,13-14,17,20,23H,4,9-12H2,1-3H3/b18-13+/t14-,17-,20-/m0/s1
SMILES:	CC[C@H]1CN2CCc3c4ccccc4[nH]c3[C@@H]2C[C@@H]1/C(=COC)/C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	3039336
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002750] Corynanthean-type alkaloids

*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
NPO3656	Ardisia pusilla	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[19039733]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21070010]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21070010]
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27359163]
NPO40904	Pausinystalia yohimbe	Species	n.a.	n.a.	Bark	n.a.	n.a.	PMID[30059216]
NPO6211	Rosa gallica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3656	Ardisia pusilla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3656	Ardisia pusilla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1603	Monostroma nitidum	Species	Monostromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6211	Rosa gallica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3656	Ardisia pusilla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO907	Dictyostelium purpureum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10499	Haplopappus paucidentatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13989	Uncaria macrophylla	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3656	Ardisia pusilla	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14694	Sickingia williamsii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6849	Lomatia arborescens	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2200	Ulmus davidiana	Species	Ulmaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6211	Rosa gallica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10315	Cestrum parqui	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11596	Lomatia ilicifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2724	Excoecaria cochinchinensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10604	Monochaetia dimorphospora	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19160	Klasea quinquefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1603	Monostroma nitidum	Species	Monostromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4870	Stephanitis pyri	Species	Tingidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8571	Actinostemma lobatum	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3135	Dendrobium lohohense	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4468	Cuspidaria pterocarpa	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8978	Stenocarpus salignus	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4229	Glossocarya calcicola	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9282	Stereocaulon colensoi	Species	Stereocaulaceae	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 NPC93956 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	288
0.1-0.2	1707
0.2-0.3	9230
0.3-0.4	20466
0.4-0.5	5698
0.5-0.6	2497
0.6-0.7	1982
0.7-0.8	706
0.8-0.85	72
0.85-0.9	25
0.9-0.95	15
0.95-1	11

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 NPC93956 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	177
0.1-0.2	505
0.2-0.3	692
0.3-0.4	1348
0.4-0.5	2482
0.5-0.6	2679
0.6-0.7	1088
0.7-0.8	173
0.8-0.85	1
0.85-0.9	3
0.9-0.95	2
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