NPASS Compound

Structure

NPC237842 OpenBabel06302215342D 49 55 0 0 1 0 0 0 0 0999 V2000 0.5519 0.6160 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9195 0.2600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5999 -0.1397 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8229 -0.6003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7234 0.1024 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8608 0.8786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1089 1.5208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7891 1.6270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2199 0.5794 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1115 1.3449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3213 1.5968 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1648 1.1643 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8634 1.1276 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2131 1.7335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8974 1.5880 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.1460 1.3318 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8779 0.5847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2948 -0.0908 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3314 0.6078 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9705 0.8923 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6435 0.5037 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3166 0.8923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3166 1.6695 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9896 0.5037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9896 -0.2734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6626 -0.6620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3357 -0.2734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3357 0.5037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6626 0.8923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0087 0.8923 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0087 1.6695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0087 -0.6620 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6817 -0.2734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7750 -0.5589 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0110 -0.2393 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.2700 0.3256 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7976 -0.1271 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7474 0.2670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8426 -0.6421 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6390 -1.3921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8877 -1.5908 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1868 -1.9434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6009 1.8857 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8081 2.6348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5662 1.9839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1861 2.2333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8009 2.4467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9128 0.3402 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 39 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 36 1 0 0 0 0 5 6 1 6 0 0 0 5 9 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 9 10 1 0 0 0 0 9 49 1 1 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 47 1 1 0 0 0 12 36 1 0 0 0 0 12 39 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 1 0 0 0 13 19 1 0 0 0 0 14 15 1 0 0 0 0 15 20 1 0 0 0 0 15 16 1 0 0 0 0 15 46 1 1 0 0 0 16 17 1 0 0 0 0 16 44 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 18 34 1 0 0 0 0 18 40 1 1 0 0 0 19 20 1 0 0 0 0 20 21 1 1 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 24 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 27 28 2 0 0 0 0 27 32 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 30 31 1 0 0 0 0 32 33 1 0 0 0 0 34 35 1 0 0 0 0 34 39 1 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 37 38 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 44 45 1 0 0 0 0 47 48 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	689.34
Volume:	674.614
LogP:	1.766
LogD:	1.757
LogS:	-3.715
# Rotatable Bonds:	13
TPSA:	151.68
# H-Bond Aceptor:	13
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.325
Synthetic Accessibility Score:	7.237
Fsp3:	0.778
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.376
MDCK Permeability:	9.042595775099471e-05
Pgp-inhibitor:	0.994
Pgp-substrate:	0.995
Human Intestinal Absorption (HIA):	0.069
20% Bioavailability (F20%):	0.013
30% Bioavailability (F30%):	0.124

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.073
Plasma Protein Binding (PPB):	22.291152954101562%
Volume Distribution (VD):	0.568
Pgp-substrate:	51.39895248413086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.936
CYP2C19-inhibitor:	0.003
CYP2C19-substrate:	0.811
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.021
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.459
CYP3A4-inhibitor:	0.614
CYP3A4-substrate:	0.707

ADMET: Excretion

Clearance (CL):	5.512
Half-life (T1/2):	0.597

ADMET: Toxicity

hERG Blockers:	0.922
Human Hepatotoxicity (H-HT):	0.925
Drug-inuced Liver Injury (DILI):	0.313
AMES Toxicity:	0.032
Rat Oral Acute Toxicity:	0.629
Maximum Recommended Daily Dose:	0.322
Skin Sensitization:	0.111
Carcinogencity:	0.018
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC237842

Natural Product ID:	NPC237842
*Common Name:**	YVPYMQHYESYLIR-HZKWNRCISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YVPYMQHYESYLIR-HZKWNRCISA-N
Standard InCHI:	InChI=1S/C36H51NO12/c1-9-37-16-33(17-42-3)23(39)13-24(45-6)36-20-14-34(41)25(46-7)15-35(49-18(2)38,27(30(36)37)28(47-8)29(33)36)26(20)31(34)48-32(40)19-10-11-21(43-4)22(12-19)44-5/h10-12,20,23-31,39,41H,9,13-17H2,1-8H3/t20-,23-,24+,25+,26-,27+,28+,29-,30-,31-,33+,34+,35-,36+/m1/s1
SMILES:	CCN1C[C@]2(COC)[C@@H](C[C@@H]([C@@]34[C@@H]5C[C@@]6([C@H](C[C@@]([C@H]5[C@H]6OC(=O)c5ccc(c(c5)OC)OC)([C@@H]([C@@H]([C@H]23)OC)[C@@H]14)OC(=O)C)OC)O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	90478913
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0003788] Aconitane-type diterpenoid alkaloids

*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
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	Okinawan soft coral	n.a.	PMID[11141107]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	Okinawan soft coral	n.a.	PMID[12398540]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[15104486]
NPO14429	0cardiopsis dassonvillei	Species	0cardiopsaceae	Bacteria	isolated from marine sediments	The estuary of Yellow River, Dongying, Shandong Province, China	n.a.	PMID[21958359]
NPO14429	0cardiopsis dassonvillei	Species	0cardiopsaceae	Bacteria	n.a.	spore	n.a.	PMID[21958359]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[26035239]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	Eukaryota	n.a.	n.a.	n.a.	PMID[30994348]
NPO13979	Tilia argentea	Species	Malvaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO18797	Hemibarbus labeo	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18797	Hemibarbus labeo	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15365	Maytenus heterophylla	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15365	Maytenus heterophylla	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18525	Diosma prama	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18797	Hemibarbus labeo	Species	Cyprinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19193	Chrysanthemum monspeliense	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16849	Melaleuca linariifolia	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14429	0cardiopsis dassonvillei	Species	0cardiopsaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO17075	Relicina sydneyensis	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13979	Tilia argentea	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16130	Streptomyces longwoodensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO18380	Marsdenia tinctoria	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4335	Anthracocystis flocculosa	Species	Ustilaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11450	Pseudoceratina purpurea	Species	Pseudoceratinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9768	Matricaria globifera	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15672	Clavularia koellikeri	Species	Clavulariidae	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 NPC237842 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	341
0.1-0.2	1469
0.2-0.3	3318
0.3-0.4	8157
0.4-0.5	11129
0.5-0.6	11930
0.6-0.7	5978
0.7-0.8	339
0.8-0.85	1
0.85-0.9	12
0.9-0.95	16
0.95-1	7

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 NPC237842 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	221
0.1-0.2	673
0.2-0.3	1423
0.3-0.4	2677
0.4-0.5	2619
0.5-0.6	1203
0.6-0.7	287
0.7-0.8	46
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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