NPASS Compound

Structure

NPC135683 OpenBabel06302215092D 62 67 0 0 1 0 0 0 0 0999 V2000 5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 0.0000 C 0 0 2 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 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 0.5000 0.0000 C 0 0 2 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 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 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 O 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 9.5263 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 11.2583 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 12.2094 -2.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.5184 -3.7601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.7972 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 12.2094 -1.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 13.7972 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.5263 -5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.6603 -6.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -5.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.7942 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9282 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 O 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 2.5981 4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7431 3.6691 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7213 3.4612 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3364 4.5827 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.6581 4.4781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8364 5.4487 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 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 -2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 35 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 21 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 23 1 6 0 0 0 16 17 1 1 0 0 0 16 21 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 19 22 1 6 0 0 0 21 20 1 1 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 31 1 0 0 0 0 25 26 1 0 0 0 0 25 34 1 6 0 0 0 26 27 1 0 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 27 32 1 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 35 36 1 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 38 40 1 0 0 0 0 40 49 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 1 0 0 0 0 43 44 1 0 0 0 0 43 51 1 1 0 0 0 44 45 1 0 0 0 0 44 49 1 0 0 0 0 45 46 1 0 0 0 0 45 47 1 0 0 0 0 47 48 1 0 0 0 0 47 50 1 0 0 0 0 48 49 1 0 0 0 0 52 51 1 6 0 0 0 52 53 1 0 0 0 0 52 59 1 0 0 0 0 53 54 1 0 0 0 0 53 62 1 1 0 0 0 54 55 1 0 0 0 0 54 61 1 6 0 0 0 55 56 1 0 0 0 0 55 60 1 1 0 0 0 56 57 1 6 0 0 0 56 59 1 0 0 0 0 57 58 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	888.4
Volume:	846.271
LogP:	0.963
LogD:	1.379
LogS:	-2.521
# Rotatable Bonds:	19
TPSA:	310.28
# H-Bond Aceptor:	20
# H-Bond Donor:	10
# Rings:	6
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.057
Synthetic Accessibility Score:	6.346
Fsp3:	0.81
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:	-6.381
MDCK Permeability:	0.0002500304253771901
Pgp-inhibitor:	0.0
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.965
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.165
Plasma Protein Binding (PPB):	41.63056945800781%
Volume Distribution (VD):	0.447
Pgp-substrate:	16.325674057006836%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.025
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.015
CYP3A4-inhibitor:	0.008
CYP3A4-substrate:	0.056

ADMET: Excretion

Clearance (CL):	1.363
Half-life (T1/2):	0.593

ADMET: Toxicity

hERG Blockers:	0.299
Human Hepatotoxicity (H-HT):	0.279
Drug-inuced Liver Injury (DILI):	0.813
AMES Toxicity:	0.064
Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.953
Skin Sensitization:	0.555
Carcinogencity:	0.935
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.97

Download Data

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

Natural Product: NPC135683

Natural Product ID:	NPC135683
*Common Name:**	WNQJURZKPAAZPV-CRWUUHLZSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WNQJURZKPAAZPV-CRWUUHLZSA-N
Standard InCHI:	InChI=1S/C42H64O20/c1-17(8-9-55-37(53)23-15-57-39(29-19(3)25(45)10-21(23)29)61-41-35(51)33(49)31(47)27(12-43)59-41)6-5-7-18(2)14-56-38(54)24-16-58-40(30-20(4)26(46)11-22(24)30)62-42-36(52)34(50)32(48)28(13-44)60-42/h15-19,21-22,25-36,39-52H,4-14H2,1-3H3/t17-,18+,19-,21-,22-,25+,26+,27-,28-,29-,30-,31-,32-,33+,34+,35-,36-,39+,40+,41+,42+/m1/s1
SMILES:	C[C@H](CCC[C@H](C)COC(=O)C1=CO[C@H]([C@@H]2C(=C)[C@H](C[C@H]12)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)CCOC(=O)C1=CO[C@H]([C@@H]2[C@H](C)[C@H](C[C@H]12)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0002049] Terpene glycosides [CHEMONTID:0004081] Iridoid O-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
NPO23522	Croton argyrophylloides	Species	Euphorbiaceae	Eukaryota	bark	Crato, Cear State, Brazil	2005-JAN	PMID[19780590]
NPO21027	Daphnia magna	Species	Daphniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20117838]
NPO15656	Fusarium equiseti	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25475336]
NPO21027	Daphnia magna	Species	Daphniidae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO4722	Peumus boldus	Species	Monimiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25014	Achillea millefolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4722	Peumus boldus	Species	Monimiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25014	Achillea millefolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25014	Achillea millefolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24648	Dryopteris sieboldii	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4722	Peumus boldus	Species	Monimiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24762	Sporothrix flocculosa	Species	Ophiostomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15656	Fusarium equiseti	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24851	Aniba gigantifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21027	Daphnia magna	Species	Daphniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25014	Achillea millefolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24801	Fagraea ceilanica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24125	Guatteria subsessilis	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23522	Croton argyrophylloides	Species	Euphorbiaceae	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 NPC135683 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	268
0.1-0.2	1645
0.2-0.3	5413
0.3-0.4	10982
0.4-0.5	11323
0.5-0.6	7648
0.6-0.7	4789
0.7-0.8	603
0.8-0.85	9
0.85-0.9	13
0.9-0.95	4
0.95-1	0

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 NPC135683 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	260
0.1-0.2	2000
0.2-0.3	4038
0.3-0.4	1935
0.4-0.5	505
0.5-0.6	298
0.6-0.7	101
0.7-0.8	13
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