NPASS Compound

Structure

NPC127639 OpenBabel06302216172D 34 36 0 0 1 0 0 0 0 0999 V2000 -9.5263 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 C 0 0 2 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 -3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 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 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 0.8660 -0.5000 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 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 34 1 0 0 0 0 4 5 2 0 0 0 0 4 33 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 12 11 1 1 0 0 0 12 13 1 0 0 0 0 12 19 1 0 0 0 0 13 14 1 0 0 0 0 13 32 1 1 0 0 0 14 15 1 6 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 21 1 6 0 0 0 19 20 1 1 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 31 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	478.15
Volume:	456.296
LogP:	1.116
LogD:	0.376
LogS:	-1.577
# Rotatable Bonds:	9
TPSA:	186.37
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.155
Synthetic Accessibility Score:	3.963
Fsp3:	0.348
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.376
MDCK Permeability:	6.2178141888580285e-06
Pgp-inhibitor:	0.003
Pgp-substrate:	0.974
Human Intestinal Absorption (HIA):	0.933
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.042
Plasma Protein Binding (PPB):	95.90218353271484%
Volume Distribution (VD):	0.52
Pgp-substrate:	5.017172336578369%

ADMET: Metabolism

CYP1A2-inhibitor:	0.333
CYP1A2-substrate:	0.033
CYP2C19-inhibitor:	0.108
CYP2C19-substrate:	0.053
CYP2C9-inhibitor:	0.363
CYP2C9-substrate:	0.317
CYP2D6-inhibitor:	0.141
CYP2D6-substrate:	0.205
CYP3A4-inhibitor:	0.174
CYP3A4-substrate:	0.071

ADMET: Excretion

Clearance (CL):	10.962
Half-life (T1/2):	0.9

ADMET: Toxicity

hERG Blockers:	0.133
Human Hepatotoxicity (H-HT):	0.275
Drug-inuced Liver Injury (DILI):	0.105
AMES Toxicity:	0.738
Rat Oral Acute Toxicity:	0.111
Maximum Recommended Daily Dose:	0.018
Skin Sensitization:	0.967
Carcinogencity:	0.046
Eye Corrosion:	0.003
Eye Irritation:	0.125
Respiratory Toxicity:	0.029

Download Data

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

Natural Product: NPC127639

Natural Product ID:	NPC127639
*Common Name:**	KOZSJSLASZUUFT-VJWFJHQPSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KOZSJSLASZUUFT-VJWFJHQPSA-N
Standard InCHI:	InChI=1S/C23H26O11/c24-11-18-20(30)22(34-19(29)6-3-12-1-4-14(25)16(27)9-12)21(31)23(33-18)32-8-7-13-2-5-15(26)17(28)10-13/h1-6,9-10,18,20-28,30-31H,7-8,11H2/b6-3+/t18-,20-,21-,22-,23-/m1/s1
SMILES:	c1cc(c(cc1/C=C/C(=O)O[C@@H]1[C@@H]([C@@H](CO)O[C@H]([C@@H]1O)OCCc1ccc(c(c1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	6915840
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11858748]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1367520]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974609]
NPO13010	Allium stipitatum	Species	Amaryllidaceae	Eukaryota	n.a.	bulb	n.a.	PMID[19093848]
NPO13010	Allium stipitatum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19093848]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21381678]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21667925]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22118684]
NPO27031	Methanosarcina barkeri	Species	Methanosarcinaceae	Archaea	n.a.	n.a.	n.a.	PMID[24669201]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24840014]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2488968]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	seed	n.a.	PMID[2610694]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26692349]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	Stems	n.a.	n.a.	PMID[31180680]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33089690]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8626236]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5137	Myristica malabarica	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5995	Spartium junceum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14614	Kopsia longiflora	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14327	Scabiosa comosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14327	Scabiosa comosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5995	Spartium junceum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14614	Kopsia longiflora	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5137	Myristica malabarica	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9917	Plagiomnium cuspidatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14327	Scabiosa comosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5995	Spartium junceum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1124	Scapania aequiloba	Species	Scapaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10031	Euphorbia antiquorum	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14327	Scabiosa comosa	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5137	Myristica malabarica	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14614	Kopsia longiflora	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12777	Laurencia pacifica	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15108	Angiopteris evecta	Species	Marattiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14454	Plectranthus lanuginosus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13460	Asphodeline damascena	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11584	Artemisia argentea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16076	Penicillium chrysogenum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2667	Acacia lasiopetala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9917	Plagiomnium cuspidatum	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27134	Euphrasia rubra	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13477	Cyberlindnera jadinii	Species	Phaffomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27031	Methanosarcina barkeri	Species	Methanosarcinaceae	Archaea	n.a.	n.a.	n.a.	Database[UNPD]
NPO8556	Eucalyptus kitsoniana	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12480	Brodiaea californica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22203	Tapinella panuoides	Species	Tapinellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15898	Streptomyces noursei	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5995	Spartium junceum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21851	Chaetomella raphigera	Species	Chaetomellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10527	Cyathula tomentosa	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26381	Bombus pascuorum	Species	Apidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13225	Spergula japonica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22101	Himantoglossum hircinum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15513	Pseudocyphellaria rubella	Species	Lobariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO255	Solanum pseudopersicum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15404	Streptomyces erythrochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15806	Rhododendron campylocarpum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14965	Lepidophorum repandum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16161	Stephania aculeata	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26951	Gymnopus androsaceus	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29322	Rhodanthe maryonii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15087	Alstonia pittieri	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13743	Populus yunnanensis	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1777	Toddalia aculeata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28240	0tholaena lemmonii	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9299.3	Hordeum vulgare var. distichon	Varieties	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15621	Lethasterias fusca	Species	Asteriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13010	Allium stipitatum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11243	Exochorda giraldii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15718	Lindera sericea	Species	Tineidae	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 NPC127639 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	306
0.1-0.2	1298
0.2-0.3	3327
0.3-0.4	8111
0.4-0.5	10031
0.5-0.6	6200
0.6-0.7	9004
0.7-0.8	3658
0.8-0.85	495
0.85-0.9	168
0.9-0.95	91
0.95-1	8

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 NPC127639 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	255
0.1-0.2	768
0.2-0.3	1625
0.3-0.4	2912
0.4-0.5	1929
0.5-0.6	1129
0.6-0.7	475
0.7-0.8	55
0.8-0.85	0
0.85-0.9	1
0.9-0.95	1
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