NPASS Compound

Structure

NPC213682 OpenBabel06302215222D 44 49 0 0 1 0 0 0 0 0999 V2000 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0132 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6010 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0132 1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 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 -1.7321 2.0000 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 -2.5981 0.5000 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 0.8660 0.5000 0.0000 C 0 0 1 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 1.7321 -1.0000 0.0000 C 0 0 2 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 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 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 -1.7321 -3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 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 0.0000 -0.0000 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 -1.5000 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 0.8660 3.5000 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 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 7 2 0 0 0 0 7 11 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 0 0 0 0 12 21 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 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 17 18 1 0 0 0 0 17 44 1 0 0 0 0 18 19 2 0 0 0 0 18 23 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 24 23 1 1 0 0 0 24 25 1 0 0 0 0 24 40 1 0 0 0 0 25 26 1 0 0 0 0 25 43 1 6 0 0 0 26 27 1 0 0 0 0 26 42 1 1 0 0 0 27 28 1 0 0 0 0 27 41 1 6 0 0 0 28 29 1 1 0 0 0 28 40 1 0 0 0 0 29 30 1 0 0 0 0 31 30 1 6 0 0 0 31 32 1 0 0 0 0 31 36 1 0 0 0 0 32 33 1 0 0 0 0 32 39 1 1 0 0 0 33 34 1 0 0 0 0 33 38 1 6 0 0 0 34 35 1 0 0 0 0 34 37 1 1 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	622.15
Volume:	561.057
LogP:	-0.168
LogD:	-0.084
LogS:	-4.611
# Rotatable Bonds:	7
TPSA:	236.43
# H-Bond Aceptor:	16
# H-Bond Donor:	7
# Rings:	6
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.159
Synthetic Accessibility Score:	4.789
Fsp3:	0.464
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.451
MDCK Permeability:	3.333888889756054e-05
Pgp-inhibitor:	0.004
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.193
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.934

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.085
Plasma Protein Binding (PPB):	75.69280242919922%
Volume Distribution (VD):	0.536
Pgp-substrate:	15.15311050415039%

ADMET: Metabolism

CYP1A2-inhibitor:	0.046
CYP1A2-substrate:	0.514
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.066
CYP2C9-inhibitor:	0.006
CYP2C9-substrate:	0.093
CYP2D6-inhibitor:	0.141
CYP2D6-substrate:	0.169
CYP3A4-inhibitor:	0.059
CYP3A4-substrate:	0.01

ADMET: Excretion

Clearance (CL):	1.258
Half-life (T1/2):	0.437

ADMET: Toxicity

hERG Blockers:	0.462
Human Hepatotoxicity (H-HT):	0.143
Drug-inuced Liver Injury (DILI):	0.603
AMES Toxicity:	0.617
Rat Oral Acute Toxicity:	0.074
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.914
Carcinogencity:	0.328
Eye Corrosion:	0.003
Eye Irritation:	0.029
Respiratory Toxicity:	0.026

Download Data

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

Natural Product: NPC213682

Natural Product ID:	NPC213682
*Common Name:**	YIADNKPSPOPEJL-YTSBCNQGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YIADNKPSPOPEJL-YTSBCNQGSA-N
Standard InCHI:	InChI=1S/C28H30O16/c1-37-17-2-10(3-18-26(17)42-9-41-18)12-6-38-15-5-13(29)16(4-11(15)20(12)31)43-28-25(36)23(34)22(33)19(44-28)8-40-27-24(35)21(32)14(30)7-39-27/h2-6,14,19,21-25,27-30,32-36H,7-9H2,1H3/t14-,19-,21+,22-,23+,24-,25-,27+,28-/m1/s1
SMILES:	COc1cc(cc2c1OCO2)c1coc2cc(c(cc2c1=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10908298
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-glycosides

*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
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[10556916]
NPO19369	Bacillus thuringiensis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	PMID[11087590]
NPO26770	Pteris multifida	Species	Pteridaceae	Eukaryota	Whole plant	n.a.	n.a.	PMID[18181575]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19406895]
NPO3494	Swietenia mahagoni	Species	Meliaceae	Eukaryota	fruits	n.a.	n.a.	PMID[19902967]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19917748]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[20932054]
NPO14077	Chamaecyparis lawsoniana	Species	Cupressaceae	Eukaryota	n.a.	leaf	n.a.	PMID[23157017]
NPO14077	Chamaecyparis lawsoniana	Species	Cupressaceae	Eukaryota	n.a.	stem	n.a.	PMID[23157017]
NPO11601	Chandonanthus hirtellus	Species	Anastrophyllaceae	Eukaryota	n.a.	Chinese liverworts	n.a.	PMID[24491225]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25043228]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25960261]
NPO13626	Aconitum karakolicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Europe PMC[305622]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[32603106]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	Antarctic	n.a.	PMID[8882433]
NPO26770	Pteris multifida	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13626	Aconitum karakolicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2756	Emerita analoga	Species	Hippidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15094	Coriaria myrtifolia	Species	Coriariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26770	Pteris multifida	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13626	Aconitum karakolicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2756	Emerita analoga	Species	Hippidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13626	Aconitum karakolicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21926	Pseudomonas aeruginosa	Species	Pseudomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3494	Swietenia mahagoni	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8866	Papaver atlanticum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16170	Xerula longipes	Species	Physalacriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2756	Emerita analoga	Species	Hippidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2312	Encephalosphaera lasiandra	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15306	Smilax japonica	Species	Smilacaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11567	Picradeniopsis absinthifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15818	Lycianthes marlipoensis	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15094	Coriaria myrtifolia	Species	Coriariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1890	Lidbeckia pectinata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12294	Kydia calycina	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12517	Tylophora cordifolia	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10624	Solidago wrightii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27787	Pseudocentrotus depressus	Species	Echinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14630	Boronia ramosa	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8611	Cornutia grandifolia	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15726	Rudbeckia subtomentosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14077	Chamaecyparis lawsoniana	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19369	Bacillus thuringiensis	Species	Bacillaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO13626	Aconitum karakolicum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7056	Pedinophyllum interruptum	Species	Plagiochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26770	Pteris multifida	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13236	Viguiera multiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11601	Chandonanthus hirtellus	Species	Anastrophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9155	Kageneckia angustifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7868	Xeromphis obovata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13360	Passiflora racemosa	Species	Passifloraceae	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 NPC213682 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	457
0.1-0.2	1838
0.2-0.3	3865
0.3-0.4	9503
0.4-0.5	8900
0.5-0.6	4565
0.6-0.7	5458
0.7-0.8	5310
0.8-0.85	1704
0.85-0.9	715
0.9-0.95	365
0.95-1	17

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 NPC213682 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	403
0.1-0.2	955
0.2-0.3	2020
0.3-0.4	2761
0.4-0.5	1787
0.5-0.6	828
0.6-0.7	252
0.7-0.8	113
0.8-0.85	17
0.85-0.9	7
0.9-0.95	7
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