NPASS Compound

Structure

NPC235490 OpenBabel06302215572D 52 58 0 0 1 0 0 0 0 0999 V2000 -2.6664 -5.2701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3735 -4.5630 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3395 -4.8218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0466 -4.1147 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -6.0125 -4.3735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7877 -3.1488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8218 -2.8900 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3678 -1.9990 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8218 -1.1080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3801 -2.1554 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2237 -3.1431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1147 -3.5971 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6730 -1.4483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7071 -1.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4483 -2.6730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7071 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6730 0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3801 1.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1213 2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1554 2.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4483 1.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8966 3.3461 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6037 4.0532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8284 2.8284 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0000 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7071 -1.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6730 -1.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3801 -2.1554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1213 -3.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1554 -3.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4483 -2.6730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8966 -4.3461 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6037 -5.0532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8284 -3.8284 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7071 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6730 0.4483 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4483 1.6730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1554 2.3801 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9990 3.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8900 3.8218 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1488 4.7877 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4417 5.4949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1147 5.0466 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8218 4.3395 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.7877 4.5983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5630 3.3735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5971 3.1147 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1431 2.2237 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5971 1.3327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 12 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 6 1 0 0 0 0 7 6 1 6 0 0 0 7 8 1 0 0 0 0 7 12 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 10 13 1 1 0 0 0 12 11 1 6 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 16 14 1 1 0 0 0 16 17 1 0 0 0 0 16 28 1 0 0 0 0 17 18 1 6 0 0 0 17 27 1 0 0 0 0 18 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 27 28 1 0 0 0 0 27 38 1 6 0 0 0 28 29 1 6 0 0 0 29 34 2 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 32 37 1 0 0 0 0 33 34 1 0 0 0 0 33 35 1 0 0 0 0 35 36 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 41 40 1 6 0 0 0 41 42 1 0 0 0 0 41 51 1 0 0 0 0 43 42 1 6 0 0 0 43 44 1 0 0 0 0 43 50 1 0 0 0 0 44 45 1 1 0 0 0 44 46 1 0 0 0 0 46 47 1 0 0 0 0 47 48 1 0 0 0 0 47 49 1 0 0 0 0 50 49 1 6 0 0 0 50 51 1 0 0 0 0 51 52 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	718.42
Volume:	746.316
LogP:	6.03
LogD:	5.094
LogS:	-3.713
# Rotatable Bonds:	10
TPSA:	118.0
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.327
Synthetic Accessibility Score:	5.572
Fsp3:	0.667
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.349
MDCK Permeability:	7.769349758746102e-05
Pgp-inhibitor:	0.991
Pgp-substrate:	0.359
Human Intestinal Absorption (HIA):	0.014
20% Bioavailability (F20%):	0.0
30% Bioavailability (F30%):	0.369

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.1
Plasma Protein Binding (PPB):	88.59292602539062%
Volume Distribution (VD):	2.303
Pgp-substrate:	7.1801886558532715%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.693
CYP2C19-inhibitor:	0.026
CYP2C19-substrate:	0.971
CYP2C9-inhibitor:	0.092
CYP2C9-substrate:	0.442
CYP2D6-inhibitor:	0.417
CYP2D6-substrate:	0.902
CYP3A4-inhibitor:	0.415
CYP3A4-substrate:	0.941

ADMET: Excretion

Clearance (CL):	15.699
Half-life (T1/2):	0.226

ADMET: Toxicity

hERG Blockers:	0.995
Human Hepatotoxicity (H-HT):	0.647
Drug-inuced Liver Injury (DILI):	0.979
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.296
Maximum Recommended Daily Dose:	0.145
Skin Sensitization:	0.53
Carcinogencity:	0.042
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.886

Download Data

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

Natural Product: NPC235490

Natural Product ID:	NPC235490
*Common Name:**	VQKTZIKAARDZIA-JZQQLPCBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VQKTZIKAARDZIA-JZQQLPCBSA-N
Standard InCHI:	InChI=1S/C42H58N2O8/c1-21-17-43(5)19-29-23(3)33(15-27(21)29)51-41(47)39-37(25-9-11-31(45)35(13-25)49-7)40(38(39)26-10-12-32(46)36(14-26)50-8)42(48)52-34-16-28-22(2)18-44(6)20-30(28)24(34)4/h9-14,21-24,27-30,33-34,37-40,45-46H,15-20H2,1-8H3/t21-,22-,23+,24+,27+,28+,29+,30+,33-,34+,37-,38+,39-,40-/m0/s1
SMILES:	C[C@H]1CN(C)C[C@@H]2[C@@H](C)[C@H](C[C@H]12)OC(=O)[C@H]1[C@H](c2ccc(c(c2)OC)O)[C@@H]([C@@H]1c1ccc(c(c1)OC)O)C(=O)O[C@@H]1C[C@@H]2[C@@H](C)CN(C)C[C@@H]2[C@H]1C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0000190] Methoxyphenols

*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
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10514316]
NPO9878	Dichapetalum gelonioides	Species	Dichapetalaceae	Eukaryota	stem bark	Philippines	n.a.	PMID[16562829]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17438049]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20961092]
NPO915	Xylaria polymorpha	Species	Xylariaceae	Eukaryota	n.a.	fruit body	n.a.	PMID[21942847]
NPO9878	Dichapetalum gelonioides	Species	Dichapetalaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24597894]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26394166]
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7492	Mucuna birdwoodiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11308	Rohdea japonica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7109	Eugenia edulis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11308	Rohdea japonica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7492	Mucuna birdwoodiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5294	Stemona ovata	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12054	Holostylis reniformis	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8150	Calibrachoa parviflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5715	Hyalodendriella betulae	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2349	Picrasma excelsa	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20351	Emericella variecolor	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12281	Aleurodiscus amorphus	Species	Stereaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11470	Sorghum caudatum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11308	Rohdea japonica	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7492	Mucuna birdwoodiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4845	Arachniodes standishii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3700	Frasera speciosa	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12165	Comanthosphace japonica	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO622	Stictina crocata	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11944	Incarvillea sinensis	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11829	Acacia ehrenbergiana	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO915	Xylaria polymorpha	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7109	Eugenia edulis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11139	Godmania aesculifolia	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4988	Lavandula stoechas	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9878	Dichapetalum gelonioides	Species	Dichapetalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6900	Koenigia divaricata	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6055	Enkianthus cernuus	Species	Ericaceae	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 NPC235490 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	267
0.1-0.2	1157
0.2-0.3	3037
0.3-0.4	9051
0.4-0.5	10702
0.5-0.6	11469
0.6-0.7	6750
0.7-0.8	263
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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 NPC235490 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	167
0.1-0.2	603
0.2-0.3	1134
0.3-0.4	2376
0.4-0.5	2722
0.5-0.6	1600
0.6-0.7	513
0.7-0.8	35
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