NPASS Compound

Structure

NPC304020 OpenBabel06302215582D 69 79 0 0 1 0 0 0 0 0999 V2000 1.6290 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6290 0.9405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2579 1.8810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2579 2.8214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0724 3.2917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8869 2.8214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8869 1.8810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0724 1.4107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2679 0.4908 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6386 -0.2081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7187 -0.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0894 -0.7115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3800 -1.6059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2999 -1.8015 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9292 -1.1026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7884 -1.4851 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4174 -0.5446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4174 0.3959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2318 0.8661 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0463 0.3959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0463 -0.5446 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2318 -1.0149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4274 -1.9348 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9102 -4.7304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2008 -5.6249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5715 -6.3238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6516 -6.1282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3609 -5.2338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9902 -4.5349 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4410 -5.0383 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8621 -7.2182 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3627 -2.0331 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.8329 -2.8476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7734 -2.8476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2436 -3.6620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7734 -4.4765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8329 -4.4765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3627 -3.6620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2436 -5.2910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.7452 -1.1739 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2318 1.8066 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6901 -2.4204 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3890 -3.0497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1935 -3.9696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8924 -4.5989 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7868 -4.3083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9824 -3.3884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2835 -2.7591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4857 -4.9376 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7702 -2.6160 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1695 -0.5160 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2032 0.3925 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6735 -0.4220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2032 -1.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6735 -2.0509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6140 -2.0509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0842 -1.2365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6140 -0.4220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0842 -2.8654 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5858 1.2517 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0724 4.2321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8145 -0.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8145 -1.4107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.8810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8145 -1.4107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8145 -0.4702 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 -1.6290 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6290 -1.8810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 1 62 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 61 1 0 0 0 0 6 7 2 0 0 0 0 7 60 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 6 0 0 0 9 52 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 51 1 0 0 0 0 13 14 2 0 0 0 0 14 50 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 16 42 1 0 0 0 0 17 22 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 41 1 0 0 0 0 20 21 2 0 0 0 0 21 40 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 6 0 0 0 23 32 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 26 31 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 32 33 1 1 0 0 0 32 40 1 0 0 0 0 33 38 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 35 36 1 0 0 0 0 36 37 2 0 0 0 0 36 39 1 0 0 0 0 37 38 1 0 0 0 0 42 43 1 1 0 0 0 42 50 1 0 0 0 0 43 48 2 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 45 46 1 0 0 0 0 46 47 2 0 0 0 0 46 49 1 0 0 0 0 47 48 1 0 0 0 0 52 53 1 1 0 0 0 52 60 1 0 0 0 0 53 58 2 0 0 0 0 53 54 1 0 0 0 0 54 55 2 0 0 0 0 55 56 1 0 0 0 0 56 57 2 0 0 0 0 56 59 1 0 0 0 0 57 58 1 0 0 0 0 62 67 2 0 0 0 0 62 63 1 0 0 0 0 63 64 2 0 0 0 0 64 65 1 0 0 0 0 65 66 2 0 0 0 0 65 69 1 0 0 0 0 66 67 1 0 0 0 0 66 68 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	922.26
Volume:	931.372
LogP:	8.257
LogD:	4.585
LogS:	-3.94
# Rotatable Bonds:	8
TPSA:	229.99
# H-Bond Aceptor:	13
# H-Bond Donor:	10
# Rings:	11
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.051
Synthetic Accessibility Score:	5.134
Fsp3:	0.107
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.568
MDCK Permeability:	5.3016378842585254e-06
Pgp-inhibitor:	0.497
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.983
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	96.9893569946289%
Volume Distribution (VD):	0.541
Pgp-substrate:	4.875030517578125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.097
CYP1A2-substrate:	0.419
CYP2C19-inhibitor:	0.933
CYP2C19-substrate:	0.038
CYP2C9-inhibitor:	0.844
CYP2C9-substrate:	0.999
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.907
CYP3A4-inhibitor:	0.323
CYP3A4-substrate:	0.213

ADMET: Excretion

Clearance (CL):	10.507
Half-life (T1/2):	0.477

ADMET: Toxicity

hERG Blockers:	0.072
Human Hepatotoxicity (H-HT):	0.622
Drug-inuced Liver Injury (DILI):	0.88
AMES Toxicity:	0.119
Rat Oral Acute Toxicity:	0.894
Maximum Recommended Daily Dose:	0.99
Skin Sensitization:	0.962
Carcinogencity:	0.028
Eye Corrosion:	0.003
Eye Irritation:	0.909
Respiratory Toxicity:	0.019

Download Data

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

Natural Product: NPC304020

Natural Product ID:	NPC304020
*Common Name:**	REQUQHNQLKHWEU-KZFZMMGWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	REQUQHNQLKHWEU-KZFZMMGWSA-N
Standard InCHI:	InChI=1S/C56H42O13/c57-33-10-4-28(5-11-33)54-49(32-19-36(60)21-37(61)20-32)50-41(22-39(63)25-46(50)68-54)53-51-42(23-40(64)26-47(51)69-56(53)30-8-14-35(59)15-9-30)52-48-31(3-1-27-2-16-43(65)44(66)17-27)18-38(62)24-45(48)67-55(52)29-6-12-34(58)13-7-29/h1-26,49,52-66H/b3-1+/t49-,52-,53+,54+,55+,56-/m1/s1
SMILES:	C(=Cc1cc(cc2c1[C@@H](c1cc(cc3c1[C@H](c1cc(cc4c1[C@@H](c1cc(cc(c1)O)O)[C@H](c1ccc(cc1)O)O4)O)[C@@H](c1ccc(cc1)O)O3)O)[C@H](c1ccc(cc1)O)O2)O)/c1ccc(c(c1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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
NPO1276	Thonningia sanguinea	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10843586]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[11076554]
NPO11304	Vitis thunbergii	Species	Vitaceae	Eukaryota	Roots	n.a.	n.a.	PMID[15730246]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	red sea	n.a.	PMID[16180827]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	Red Sea	n.a.	PMID[17190441]
NPO1276	Thonningia sanguinea	Species	Balanophoraceae	Eukaryota	Subaerial Parts	n.a.	n.a.	PMID[30207720]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[3572416]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8778242]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9461648]
NPO9038	Aconitum burnatii	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4980	Lycopodium erythraeum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12049	Lecania gerlachei	Species	Ramalinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1276	Thonningia sanguinea	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10313	Plantago arborescens	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11941	Helleborus serbicus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16596	Dysoxylum schiffneri	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5239	Hyrtios erecta	Species	Thorectidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20597	Phascolion strombus	Species	Phascolionidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO222	Phebalium drummondii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8519	Garcinia andamanica	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11304	Vitis thunbergii	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5899	Ainsliaea uniflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6028	Laurencia pinnatifida	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10086	Scrophularia scorodonia	Species	Scrophulariaceae	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 NPC304020 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	526
0.1-0.2	1695
0.2-0.3	4641
0.3-0.4	12191
0.4-0.5	6060
0.5-0.6	4535
0.6-0.7	7641
0.7-0.8	4365
0.8-0.85	744
0.85-0.9	234
0.9-0.95	61
0.95-1	4

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 NPC304020 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	427
0.1-0.2	923
0.2-0.3	1855
0.3-0.4	2784
0.4-0.5	1605
0.5-0.6	946
0.6-0.7	518
0.7-0.8	86
0.8-0.85	4
0.85-0.9	2
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