NPASS Compound

Structure

NPC107225 OpenBabel06302215172D 48 50 0 0 1 0 0 0 0 0999 V2000 8.1168 -1.3824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0952 -1.7719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2470 -1.0818 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2254 -1.4713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3772 -0.7813 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9584 -1.1725 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4496 -1.4361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8885 -1.5527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3167 -1.5136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7767 -1.3217 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2737 -2.2925 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3086 -0.9912 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9469 -0.5467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8938 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8938 1.0934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9469 1.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3086 2.0846 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5623 2.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8811 3.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9463 4.1763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2652 5.2221 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7767 2.4151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3167 2.6070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8885 2.6461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4496 2.5295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9584 2.2659 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5889 3.1591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3772 1.8747 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6750 1.3851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8296 0.8332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8296 0.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6750 -0.2917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4010 0.1275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4010 0.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3479 -0.4192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9128 0.1113 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2254 2.5647 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0519 3.6443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0302 4.0338 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.9000 4.3343 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9469 1.6401 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8407 1.6401 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5623 -1.7903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8811 -2.8362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9463 -3.0829 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.1349 -3.6352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 32 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 12 45 1 1 0 0 0 13 42 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 16 1 0 0 0 0 15 44 1 0 0 0 0 16 17 1 0 0 0 0 16 41 2 0 0 0 0 17 18 1 6 0 0 0 17 22 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 26 28 1 0 0 0 0 28 29 1 0 0 0 0 28 37 1 1 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 31 36 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 33 35 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 41 42 1 0 0 0 0 41 43 1 0 0 0 0 45 46 1 0 0 0 0 46 47 2 0 0 0 0 46 48 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	670.42
Volume:	711.358
LogP:	8.498
LogD:	5.084
LogS:	-2.547
# Rotatable Bonds:	10
TPSA:	185.56
# H-Bond Aceptor:	10
# H-Bond Donor:	8
# Rings:	6
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.16
Synthetic Accessibility Score:	6.196
Fsp3:	0.632
Lipinski Rule-of-5:	Rejected
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:	-5.223
MDCK Permeability:	3.4509645047364756e-05
Pgp-inhibitor:	0.814
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.01
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.115
Plasma Protein Binding (PPB):	100.36067962646484%
Volume Distribution (VD):	2.651
Pgp-substrate:	0.7485151290893555%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.959
CYP2C19-inhibitor:	0.291
CYP2C19-substrate:	0.106
CYP2C9-inhibitor:	0.13
CYP2C9-substrate:	0.987
CYP2D6-inhibitor:	0.337
CYP2D6-substrate:	0.176
CYP3A4-inhibitor:	0.193
CYP3A4-substrate:	0.168

ADMET: Excretion

Clearance (CL):	3.421
Half-life (T1/2):	0.049

ADMET: Toxicity

hERG Blockers:	0.234
Human Hepatotoxicity (H-HT):	0.819
Drug-inuced Liver Injury (DILI):	0.911
AMES Toxicity:	0.5
Rat Oral Acute Toxicity:	0.979
Maximum Recommended Daily Dose:	0.988
Skin Sensitization:	0.953
Carcinogencity:	0.09
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.803

Download Data

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

Natural Product: NPC107225

Natural Product ID:	NPC107225
*Common Name:**	MMNOSSIKVRRNRZ-YXTQZPCGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MMNOSSIKVRRNRZ-YXTQZPCGSA-N
Standard InCHI:	InChI=1S/C38H58N2O8/c1-5-7-15-25-17-11-9-13-23(3)36(48-38(40)46)28-21-31(43)34(32(44)22-28)26(16-8-6-2)18-12-10-14-24(4)35(47-37(39)45)27-19-29(41)33(25)30(42)20-27/h19-26,35-36,41-44H,5-18H2,1-4H3,(H2,39,45)(H2,40,46)/t23-,24-,25-,26+,35+,36+/m0/s1
SMILES:	CCCC[C@H]1CCCC[C@H](C)[C@H](c2cc(c([C@H](CCCC)CCCC[C@H](C)[C@H](c3cc(c1c(c3)O)O)OC(=N)O)c(c2)O)O)OC(=N)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0004647] 1-hydroxy-4-unsubstituted benzenoids

*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]
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]
NPO7240	Osteospermum oppositifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
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]
NPO1969	Streptomyces pilosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8811	Cytisus prolifer	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28833	Eleutherococcus sieboldianus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19804	Lycopodium saururus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5335	0stoc sp	Species	0stocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO834	Peperomia clusiifolia	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8623	Anneissia japonica	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9705	Meyerozyma guilliermondii	Species	Debaryomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7788	Rana catesbeiana	Species	Ranidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3613	Eriobotrya deflexa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4541	Capnella lacertiliensis	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19541	Smilax moranensis	Species	Smilacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8305	Katsuwonus pelamis	Species	Scombridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1537	Vaccinium arctostaphylos	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8426	Tinospora rumphii	Species	Menispermaceae	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 NPC107225 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	216
0.1-0.2	1222
0.2-0.3	3489
0.3-0.4	11072
0.4-0.5	8561
0.5-0.6	7438
0.6-0.7	8756
0.7-0.8	1893
0.8-0.85	38
0.85-0.9	8
0.9-0.95	4
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 NPC107225 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	171
0.1-0.2	805
0.2-0.3	1421
0.3-0.4	2780
0.4-0.5	2085
0.5-0.6	1302
0.6-0.7	557
0.7-0.8	28
0.8-0.85	1
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