NPASS Compound

Structure

NPC56592 OpenBabel06302215112D 43 50 0 0 1 0 0 0 0 0999 V2000 2.0888 2.5202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7689 1.3321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7688 0.4442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5377 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5377 -0.8884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7688 -1.3326 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0227 -1.7898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1534 -1.9986 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5379 -2.6647 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9225 -1.9987 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3070 -1.3326 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0764 -0.8884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0764 -0.0001 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8458 0.4441 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8458 -0.4699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3835 0.4441 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.1524 0.8880 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3835 1.3319 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6152 1.7761 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6152 2.6636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1152 3.3968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5002 4.1964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3852 4.2628 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0002 4.9296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8458 1.3319 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0765 1.7761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3071 1.3320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4627 1.6063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1782 2.4819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7943 3.1661 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9408 0.8881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0202 0.8881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4627 0.1698 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3071 0.4441 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0962 -1.7882 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.8884 0.0000 C 0 0 2 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 -0.7891 0.4556 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7892 -1.3439 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9200 1.8811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5799 1.2871 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1045 2.7497 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9489 3.0242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 40 1 0 0 0 0 3 37 1 0 0 0 0 3 4 1 0 0 0 0 4 34 1 0 0 0 0 4 5 2 0 0 0 0 5 11 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 1 0 0 0 6 8 1 0 0 0 0 6 36 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 35 1 1 0 0 0 13 12 1 6 0 0 0 13 14 1 0 0 0 0 13 34 1 0 0 0 0 14 25 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 17 1 1 0 0 0 18 19 1 0 0 0 0 19 20 1 6 0 0 0 19 25 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 25 26 1 1 0 0 0 26 27 1 0 0 0 0 27 34 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 28 31 1 0 0 0 0 29 30 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 34 33 1 1 0 0 0 36 37 1 0 0 0 0 36 39 1 1 0 0 0 37 38 2 0 0 0 0 40 41 2 0 0 0 0 40 42 1 0 0 0 0 42 43 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	594.25
Volume:	580.319
LogP:	2.884
LogD:	2.384
LogS:	-4.502
# Rotatable Bonds:	6
TPSA:	153.5
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.213
Synthetic Accessibility Score:	6.552
Fsp3:	0.727
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.336
MDCK Permeability:	7.125496631488204e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.492
Human Intestinal Absorption (HIA):	0.046
20% Bioavailability (F20%):	0.832
30% Bioavailability (F30%):	0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.865
Plasma Protein Binding (PPB):	50.127601623535156%
Volume Distribution (VD):	0.436
Pgp-substrate:	23.87502098083496%

ADMET: Metabolism

CYP1A2-inhibitor:	0.037
CYP1A2-substrate:	0.861
CYP2C19-inhibitor:	0.221
CYP2C19-substrate:	0.464
CYP2C9-inhibitor:	0.202
CYP2C9-substrate:	0.012
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.039
CYP3A4-inhibitor:	0.918
CYP3A4-substrate:	0.472

ADMET: Excretion

Clearance (CL):	7.644
Half-life (T1/2):	0.03

ADMET: Toxicity

hERG Blockers:	0.332
Human Hepatotoxicity (H-HT):	0.228
Drug-inuced Liver Injury (DILI):	0.251
AMES Toxicity:	0.037
Rat Oral Acute Toxicity:	0.271
Maximum Recommended Daily Dose:	0.905
Skin Sensitization:	0.527
Carcinogencity:	0.388
Eye Corrosion:	0.003
Eye Irritation:	0.014
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC56592

Natural Product ID:	NPC56592
*Common Name:**	IXFDRCYQIQGSHW-YJZJOYDFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IXFDRCYQIQGSHW-YJZJOYDFSA-N
Standard InCHI:	InChI=1S/C33H38O10/c1-12(28(38)41-5)23-24-26-31(4,27(37)25(23)36)20-8-21(20)32(26,40)9-22-30(3)17-6-14(17)16(11-42-13(2)35)18(30)7-19-15(10-34)29(39)43-33(19,22)24/h14,16-18,20-22,27,34,37,40H,6-11H2,1-5H3/b23-12-/t14-,16-,17-,18+,20-,21+,22+,27+,30+,31+,32+,33+/m1/s1
SMILES:	C/C(=C/1C2=C3[C@](C)([C@@H]4C[C@@H]4[C@]3(C[C@H]3[C@@]4(C)[C@@H]5C[C@@H]5[C@@H](COC(=O)C)[C@@H]4CC4=C(CO)C(=O)O[C@]234)O)[C@H](C1=O)O)/C(=O)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	54671541
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	Spanish		DOI[10.1021/jf00010a019]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		DOI[10.1021/jf00016a013]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	Germany		DOI[10.1021/jf00016a013]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	Italy		DOI[10.1021/jf00016a013]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	Turkey		DOI[10.1111/j.1745-4557.2003.tb00250.x]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		DOI[10.17660/ActaHortic.2003.610.16]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[10794642]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[10820090]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[11754554]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[15315387]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[16076125]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[16920856]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[19358604]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[21190690]
NPO6674	Burkholderia ambifaria	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	PMID[22988812]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[23394984]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	Germany		PMID[23394984]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	New Zealand		PMID[23394984]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[2413754]
NPO17386	Securidaca longepedunculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24216090]
NPO11257	Momordica dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30673219]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	Fruits	n.a.		PMID[9542132]
NPO11097	Lepidium apetalum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11097	Lepidium apetalum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11257	Momordica dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11257	Momordica dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11097	Lepidium apetalum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11097	Lepidium apetalum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12891	Minasia alpestris	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3740	Trisetum flavescens	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1185	Stereocaulon strictum	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3385	Cassine transvaalensis	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO468	Dryopteris oligophlebia	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9512	Phlomis fruticosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11097	Lepidium apetalum	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17386	Securidaca longepedunculata	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6674	Burkholderia ambifaria	Species	Burkholderiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19898	Stevia lucida	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9928	Cephalaria cilicica	Species	Caprifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12998	Salvia rubescens	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9040	Elsinoe annonae	Species	Elsinoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12192	Coronilla scorpioides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11815	Mikania hirsutissima	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7345	Ptilonia magellanica	Species	Bonnemaisoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10399	Manfreda virginica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8484	Codonopsis lanceolata	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7048	Eucalyptus rariflora	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16164	Podocarpus urbani	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9307	Ficus indica	Species	Ficidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO936	Pinalia spicata	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2300	Actinidia deliciosa	Species	Actinidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5827	Dalea tuberculata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5013	Loranthus spicatus	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10738	Cotoneaster horizontalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11555	Pterocaulon purpurascens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5392	Pachycereus pecten-aboriginum	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11257	Momordica dioica	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6256	Eucalyptus umbra	Species	Myrtaceae	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 NPC56592 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	312
0.1-0.2	1797
0.2-0.3	5572
0.3-0.4	8864
0.4-0.5	12780
0.5-0.6	8244
0.6-0.7	4301
0.7-0.8	753
0.8-0.85	31
0.85-0.9	32
0.9-0.95	9
0.95-1	2

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 NPC56592 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	276
0.1-0.2	2141
0.2-0.3	3911
0.3-0.4	1864
0.4-0.5	569
0.5-0.6	213
0.6-0.7	149
0.7-0.8	27
0.8-0.85	0
0.85-0.9	0
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