NPASS Compound

Structure

NPC57338 OpenBabel06302216112D 43 48 0 0 1 0 0 0 0 0999 V2000 -3.3934 3.9184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 2.9388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5451 2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 2.9388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5451 1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 0.9796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9796 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8484 1.4694 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6967 0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5451 -1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6967 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -1.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 -2.4490 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8484 -3.4286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.9184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -4.8980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 -5.3878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 -4.8980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 -3.9184 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5451 -3.4286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5451 -2.4490 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3934 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2418 -2.4490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0901 -1.9592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0901 -0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2418 -0.4898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3934 -0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9385 -0.4898 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 -1.9592 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6967 -0.9796 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8484 -6.3673 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -3.4286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 -0.4898 0.0000 C 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 1.6967 -2.9388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3934 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8484 2.4490 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6967 3.9184 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 4 43 1 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 6 10 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 39 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 42 1 6 0 0 0 12 13 1 0 0 0 0 13 38 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 41 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 40 1 0 0 0 0 17 38 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 18 34 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 37 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 36 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 34 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 33 1 0 0 0 0 31 32 1 0 0 0 0 34 35 1 6 0 0 0 38 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	592.16
Volume:	567.238
LogP:	2.781
LogD:	2.014
LogS:	-4.674
# Rotatable Bonds:	4
TPSA:	209.76
# H-Bond Aceptor:	12
# H-Bond Donor:	9
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.167
Synthetic Accessibility Score:	4.554
Fsp3:	0.226
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.864
MDCK Permeability:	4.860813078266801e-06
Pgp-inhibitor:	0.044
Pgp-substrate:	0.036
Human Intestinal Absorption (HIA):	0.821
20% Bioavailability (F20%):	0.918
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	93.30353546142578%
Volume Distribution (VD):	0.376
Pgp-substrate:	6.2518744468688965%

ADMET: Metabolism

CYP1A2-inhibitor:	0.038
CYP1A2-substrate:	0.245
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.052
CYP2C9-inhibitor:	0.784
CYP2C9-substrate:	0.971
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.208
CYP3A4-inhibitor:	0.189
CYP3A4-substrate:	0.561

ADMET: Excretion

Clearance (CL):	8.444
Half-life (T1/2):	0.677

ADMET: Toxicity

hERG Blockers:	0.082
Human Hepatotoxicity (H-HT):	0.118
Drug-inuced Liver Injury (DILI):	0.562
AMES Toxicity:	0.288
Rat Oral Acute Toxicity:	0.588
Maximum Recommended Daily Dose:	0.934
Skin Sensitization:	0.938
Carcinogencity:	0.024
Eye Corrosion:	0.003
Eye Irritation:	0.888
Respiratory Toxicity:	0.037

Download Data

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

Natural Product: NPC57338

Natural Product ID:	NPC57338
*Common Name:**	JPFCOVZKLAXXOE-XBNSMERZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JPFCOVZKLAXXOE-XBNSMERZSA-N
Standard InCHI:	InChI=1S/C31H28O12/c1-41-31-20(37)6-13(7-21(31)38)28-22(39)10-16-17(34)11-19(36)25(30(16)43-28)26-24-18(35)8-15(33)9-23(24)42-29(27(26)40)12-2-4-14(32)5-3-12/h2-9,11,22,26-29,32-40H,10H2,1H3/t22-,26-,27-,28?,29-/m1/s1
SMILES:	COc1c(cc(cc1O)C1[C@@H](Cc2c(cc(c([C@H]3c4c(cc(cc4O[C@H](c4ccc(cc4)O)[C@@H]3O)O)O)c2O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	108065
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(01)00320-X]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[10336650]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11738417]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679315]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16252923]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	fruit	n.a.	PMID[16417304]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	branch	n.a.	PMID[17202693]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[17624889]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18611049]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18768384]
NPO7298.2	Brassica napus var. napus	Varieties	Brassicaceae	Eukaryota	n.a.	KWS Saat AG and NPZ Saatzucht, Germany	2004-2005	PMID[19086241]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19476340]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21462031]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	calyx	n.a.	PMID[21561086]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21912858]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	cone	n.a.	PMID[22111577]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	flower	n.a.	PMID[22166201]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23790907]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	fruit	n.a.	PMID[24086493]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24948953]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25564559]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29154541]
NPO3912	Areca catechu	Species	Arecaceae	Eukaryota	n.a.	fruit	n.a.	Database[Article]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Root	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7298.2	Brassica napus var. napus	Varieties	Brassicaceae	Eukaryota	Roots	n.a.		Database[FooDB]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7298.2	Brassica napus var. napus	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3912	Areca catechu	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3912	Areca catechu	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23418	Testa arachidis hypogaeae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO19584	Pericarpium citri reticulatae	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]
NPO7298.2	Brassica napus var. napus	Varieties	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26422	Rubus chingii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3912	Areca catechu	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3912	Areca catechu	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO13879	Humulus lupulus	Species	Cannabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26422	Rubus chingii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18930	Rubus coreanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18930	Rubus coreanus	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26422	Rubus chingii	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15095	Hippophae rhamnoides	Species	Elaeagnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18296	Diospyros kaki	Species	Ebenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26293	Ginkgo biloba	Species	Ginkgoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3912	Areca catechu	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13879	Humulus lupulus	Species	Cannabaceae	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 NPC57338 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	493
0.1-0.2	1695
0.2-0.3	4642
0.3-0.4	11435
0.4-0.5	6699
0.5-0.6	4200
0.6-0.7	6196
0.7-0.8	5684
0.8-0.85	909
0.85-0.9	568
0.9-0.95	144
0.95-1	32

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 NPC57338 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	417
0.1-0.2	897
0.2-0.3	1975
0.3-0.4	2718
0.4-0.5	1563
0.5-0.6	855
0.6-0.7	582
0.7-0.8	131
0.8-0.85	7
0.85-0.9	5
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