NPASS Compound

Structure

CID217981 OpenBabel06191716012D 33 36 0 0 1 0 0 0 0 0999 V2000 2.9538 0.5674 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6087 2.2713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4067 0.3758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6424 -0.5654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1561 -0.0110 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2758 3.2069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9572 1.6878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6595 -0.0005 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3293 0.9375 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3673 2.2655 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9849 -0.1926 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6166 1.6974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9888 -0.5719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9406 2.8299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6976 2.8275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6536 -0.1949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6281 0.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0428 3.2057 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3407 1.6935 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3302 -0.5709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3781 2.8287 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6645 0.5604 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9522 2.0742 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9733 0.5631 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.3342 -0.1940 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6862 2.0714 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2825 -0.5646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2627 0.5814 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0457 3.9353 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6889 1.6985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8930 -0.1786 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 -0.6192 2.2540 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 2 10 1 0 0 0 0 3 31 1 0 0 0 0 4 5 1 0 0 0 0 5 31 1 0 0 0 0 6 14 1 0 0 0 0 6 21 1 0 0 0 0 7 12 2 0 0 0 0 7 32 1 0 0 0 0 8 13 2 0 0 0 0 8 33 1 0 0 0 0 9 1 1 6 0 0 0 9 19 1 0 0 0 0 9 22 1 0 0 0 0 10 15 2 0 0 0 0 10 30 1 0 0 0 0 11 4 1 6 0 0 0 11 20 1 0 0 0 0 11 24 1 0 0 0 0 12 17 1 0 0 0 0 12 23 1 0 0 0 0 13 16 1 0 0 0 0 13 25 1 0 0 0 0 14 23 2 0 0 0 0 14 32 1 0 0 0 0 15 18 1 0 0 0 0 15 26 1 0 0 0 0 16 22 2 3 0 0 0 16 27 1 0 0 0 0 17 24 2 3 0 0 0 17 28 1 0 0 0 0 18 21 2 3 0 0 0 18 29 1 0 0 0 0 19 26 2 0 0 0 0 19 30 1 0 0 0 0 20 25 2 0 0 0 0 20 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	506.09
Volume:	453.191
LogP:	3.143
LogD:	2.609
LogS:	-5.645
# Rotatable Bonds:	3
TPSA:	139.11
# H-Bond Aceptor:	10
# H-Bond Donor:	3
# Rings:	4
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.493
Synthetic Accessibility Score:	6.015
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.17
MDCK Permeability:	2.2130085199023597e-05
Pgp-inhibitor:	0.061
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.022
Plasma Protein Binding (PPB):	94.76539611816406%
Volume Distribution (VD):	1.38
Pgp-substrate:	9.541494369506836%

ADMET: Metabolism

CYP1A2-inhibitor:	0.69
CYP1A2-substrate:	0.446
CYP2C19-inhibitor:	0.61
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.822
CYP2C9-substrate:	0.085
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.198
CYP3A4-inhibitor:	0.472
CYP3A4-substrate:	0.266

ADMET: Excretion

Clearance (CL):	2.929
Half-life (T1/2):	0.088

ADMET: Toxicity

hERG Blockers:	0.019
Human Hepatotoxicity (H-HT):	0.918
Drug-inuced Liver Injury (DILI):	0.986
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.01
Maximum Recommended Daily Dose:	0.896
Skin Sensitization:	0.031
Carcinogencity:	0.251
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.664

Download Data

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

Natural Product: NPC217981

Natural Product ID:	NPC217981
*Common Name:**	Tenuecyclamide C
IUPAC Name:	n.a.
Synonyms:	tenuecyclamide C
Standard InCHIKey:	DMFUPHMBLSJHNR-ONGXEEELSA-N
Standard InCHI:	InChI=1S/C20H22N6O4S3/c1-9-19-26-15(10(2)30-19)18(29)21-6-14-23-12(7-32-14)17(28)24-11(4-5-31-3)20-25-13(8-33-20)16(27)22-9/h7-9,11H,4-6H2,1-3H3,(H,21,29)(H,22,27)(H,24,28)/t9-,11-/m0/s1
SMILES:	CSCC[C@@H]1N=C(O)c2csc(n2)CN=C(O)c2nc([C@@H](N=C(c3nc1sc3)O)C)oc2C
Synthetic Gene Cluster:	BGC0000480;
ChEMBL Identifier:	CHEMBL518880
PubChem CID:	10720367
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000064] Macrolactams

*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
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	DOI[10.1021/jo00416a020]
NPO3613	Eriobotrya deflexa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11473413]
NPO4541	Capnella lacertiliensis	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608844]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	leaves	n.a.	n.a.	PMID[17243726]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24476550]
NPO40251	0stoc spongiaeforme var. tenue	Strain	0stocaceae	Bacteria	n.a.	n.a.	n.a.	PMID[9784161]
NPO8305	Katsuwonus pelamis	Species	Scombridae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3613	Eriobotrya deflexa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12744	Ajuga nipponensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10879	Lasius meridionalis	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4198	Ungernia vvedenskyi	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12744	Ajuga nipponensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23436	Cladrastis sikokiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8811	Cytisus prolifer	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1969	Streptomyces pilosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19804	Lycopodium saururus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28833	Eleutherococcus sieboldianus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO834	Peperomia clusiifolia	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5335	0stoc sp	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8623	Anneissia japonica	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9705	Meyerozyma guilliermondii	Species	Debaryomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3613	Eriobotrya deflexa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7788	Rana catesbeiana	Species	Ranidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19541	Smilax moranensis	Species	Smilacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4541	Capnella lacertiliensis	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1537	Vaccinium arctostaphylos	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8305	Katsuwonus pelamis	Species	Scombridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8426	Tinospora rumphii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7240	Osteospermum oppositifolium	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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2588	Organism	Paracentrotus lividus	Paracentrotus lividus	ED100	=	9.0	uM	PMID[490412]

☑ 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 NPC217981 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	574
0.1-0.2	24943
0.2-0.3	13562
0.3-0.4	3306
0.4-0.5	203
0.5-0.6	82
0.6-0.7	16
0.7-0.8	1
0.8-0.85	2
0.85-0.9	0
0.9-0.95	2
0.95-1	6

Similarity Score	Similarity Level	Natural Product ID
0.9796	High Similarity	NPC201014
0.9796	High Similarity	NPC110129
0.9664	High Similarity	NPC222391
0.9474	High Similarity	NPC34319
0.9346	High Similarity	NPC256912
0.8387	Intermediate Similarity	NPC50274
0.8239	Intermediate Similarity	NPC237219
0.7461	Intermediate Similarity	NPC235866
0.6928	Remote Similarity	NPC51692
0.679	Remote Similarity	NPC103268
0.6752	Remote Similarity	NPC89592
0.6711	Remote Similarity	NPC214375
0.6584	Remote Similarity	NPC74917
0.6564	Remote Similarity	NPC315872
0.6543	Remote Similarity	NPC120917
0.6516	Remote Similarity	NPC135558
0.645	Remote Similarity	NPC475390
0.6392	Remote Similarity	NPC267605
0.6141	Remote Similarity	NPC164006
0.5979	Remote Similarity	NPC132662
0.5771	Remote Similarity	NPC469801
0.576	Remote Similarity	NPC315061
0.5748	Remote Similarity	NPC49195
0.5743	Remote Similarity	NPC315411
0.5638	Remote Similarity	NPC475554
0.5635	Remote Similarity	NPC96016

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 NPC217981 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	185
0.1-0.2	2111
0.2-0.3	4162
0.3-0.4	2413
0.4-0.5	240
0.5-0.6	38
0.6-0.7	1
0.7-0.8	0
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
0.6564	Remote Similarity	NPD6444	Clinical (unspecified phase)
0.5968	Remote Similarity	NPD2623	Phase 1
0.5659	Remote Similarity	NPD7896	Approved

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