NPASS Compound

Structure

NPC25761 OpenBabel06302215402D 54 59 0 0 1 0 0 0 0 0999 V2000 10.3923 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -1.0000 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 7.7942 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -1.0000 0.0000 O 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 5.1962 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 0.0000 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 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 8.6603 2.0000 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 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 3.5000 0.0000 O 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 5.0000 0.0000 C 0 0 0 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 2.5981 3.5000 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 1.7321 5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 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 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 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 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 -0.0000 -1.0000 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 -1.0000 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 0.0000 -0.0000 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 2.5981 -1.5000 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 12.9904 0.5000 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 54 1 0 0 0 0 4 5 2 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 11 12 1 0 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 15 1 0 0 0 0 14 53 1 1 0 0 0 15 16 1 0 0 0 0 15 52 1 6 0 0 0 16 17 1 0 0 0 0 16 40 1 1 0 0 0 17 18 1 0 0 0 0 17 19 1 6 0 0 0 19 20 1 0 0 0 0 20 30 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 39 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 38 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 31 36 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 37 1 0 0 0 0 35 36 1 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 43 1 0 0 0 0 43 44 2 0 0 0 0 44 45 1 0 0 0 0 45 50 2 0 0 0 0 45 46 1 0 0 0 0 46 47 2 0 0 0 0 47 48 1 0 0 0 0 48 49 2 0 0 0 0 48 51 1 0 0 0 0 49 50 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	740.17
Volume:	716.158
LogP:	4.398
LogD:	2.772
LogS:	-4.155
# Rotatable Bonds:	12
TPSA:	242.88
# H-Bond Aceptor:	15
# H-Bond Donor:	7
# Rings:	6
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.08
Synthetic Accessibility Score:	4.507
Fsp3:	0.154
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.997
MDCK Permeability:	2.257762389490381e-05
Pgp-inhibitor:	0.016
Pgp-substrate:	0.22
Human Intestinal Absorption (HIA):	0.157
20% Bioavailability (F20%):	0.985
30% Bioavailability (F30%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.01
Plasma Protein Binding (PPB):	101.37943267822266%
Volume Distribution (VD):	0.549
Pgp-substrate:	1.001007318496704%

ADMET: Metabolism

CYP1A2-inhibitor:	0.593
CYP1A2-substrate:	0.015
CYP2C19-inhibitor:	0.804
CYP2C19-substrate:	0.039
CYP2C9-inhibitor:	0.688
CYP2C9-substrate:	0.961
CYP2D6-inhibitor:	0.87
CYP2D6-substrate:	0.365
CYP3A4-inhibitor:	0.653
CYP3A4-substrate:	0.094

ADMET: Excretion

Clearance (CL):	5.499
Half-life (T1/2):	0.908

ADMET: Toxicity

hERG Blockers:	0.227
Human Hepatotoxicity (H-HT):	0.149
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.679
Rat Oral Acute Toxicity:	0.084
Maximum Recommended Daily Dose:	0.133
Skin Sensitization:	0.961
Carcinogencity:	0.163
Eye Corrosion:	0.003
Eye Irritation:	0.681
Respiratory Toxicity:	0.009

Download Data

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

Natural Product: NPC25761

Natural Product ID:	NPC25761
*Common Name:**	YXXQUJGFZPLXJV-TXPPTBEJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YXXQUJGFZPLXJV-TXPPTBEJSA-N
Standard InCHI:	InChI=1S/C39H32O15/c40-23-9-1-20(2-10-23)5-15-30(45)50-19-29-33(47)35(49)38(53-31(46)16-6-21-3-11-24(41)12-4-21)39(52-29)54-37-34(48)32-27(44)17-26(43)18-28(32)51-36(37)22-7-13-25(42)14-8-22/h1-18,29,33,35,38-44,47,49H,19H2/b15-5+,16-6-/t29-,33-,35+,38-,39+/m1/s1
SMILES:	c1cc(ccc1/C=C/C(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)Oc1c(=O)c2c(cc(cc2oc1c1ccc(cc1)O)O)O)OC(=O)/C=Cc1ccc(cc1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10439992
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003678] Flavonoid 3-O-p-coumaroyl 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
NPO6850	Typha domingensis	Species	Typhaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[21417376]
NPO7622	Monanchora pulchra	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21848268]
NPO7622	Monanchora pulchra	Species	Crambeidae	Eukaryota	n.a.	Urup Island (4557,9 N; 15044,9 E; depth 66 m)	2008-AUG	PMID[21848268]
NPO17226	Burkholderia pyrrocinia	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[4955234]
NPO5082	Cycas revoluta	Species	Cycadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3124	Gloiopeltis furcata	Species	Endocladiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5082	Cycas revoluta	Species	Cycadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3124	Gloiopeltis furcata	Species	Endocladiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3124	Gloiopeltis furcata	Species	Endocladiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5082	Cycas revoluta	Species	Cycadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7622	Monanchora pulchra	Species	Crambeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17226	Burkholderia pyrrocinia	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2968	Anthopleura xanthogrammica	Species	Actiniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3756	Munronia delavayi	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2609	Neonectria candida	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO115	Eutreptia viridis	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6130	Mammillaria magnimamma	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4816	Cycas armstrongii	Species	Cycadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3124	Gloiopeltis furcata	Species	Endocladiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18463	Plectocephalus chilensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6850	Typha domingensis	Species	Typhaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO291	Suillus bovinus	Species	Suillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4293	Allium neapolitanum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6302	Licaria armeniaca	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10870	Trichilia hirta	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25775	Dasystenella acanthina	Species	Primnoidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5082	Cycas revoluta	Species	Cycadaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1897	Ephedra aphylla	Species	Ephedraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3419	Quercus suber	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19333	Byssothecium obiones	Species	Massarinaceae	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 NPC25761 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	422
0.1-0.2	1760
0.2-0.3	4244
0.3-0.4	9454
0.4-0.5	8826
0.5-0.6	4714
0.6-0.7	5760
0.7-0.8	5211
0.8-0.85	1329
0.85-0.9	544
0.9-0.95	347
0.95-1	86

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 NPC25761 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	381
0.1-0.2	933
0.2-0.3	1943
0.3-0.4	2699
0.4-0.5	1892
0.5-0.6	887
0.6-0.7	262
0.7-0.8	112
0.8-0.85	25
0.85-0.9	11
0.9-0.95	5
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