NPASS Compound

Structure

NPC2789 OpenBabel06302215562D 37 42 0 0 1 0 0 0 0 0999 V2000 -2.3557 -1.6400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4896 -1.1400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6236 -1.6400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4896 -0.1400 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6236 0.3600 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6236 1.0801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.4402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6236 1.0801 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6236 2.0801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6236 0.3600 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2472 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8709 0.3600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8709 1.0801 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7369 0.5801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2472 1.4402 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2472 2.1603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8709 2.5203 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4945 2.1603 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1524 1.4072 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0330 0.4144 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8332 -0.1855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2333 -0.9856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2262 -1.1050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7527 0.2076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8721 1.2004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0719 1.8002 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7595 1.1515 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0575 0.9912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4945 1.4402 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0578 2.2664 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9823 2.7962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7354 3.4541 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0074 3.0187 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8709 3.5203 0.0000 O 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 -0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -0.8660 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 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 35 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 15 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 6 0 0 0 10 35 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 29 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 1 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 34 1 6 0 0 0 18 29 1 0 0 0 0 18 33 1 1 0 0 0 18 19 1 0 0 0 0 19 20 1 1 0 0 0 19 26 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 24 1 0 0 0 0 24 25 1 0 0 0 0 26 25 1 6 0 0 0 26 27 1 0 0 0 0 26 31 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 6 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 35 36 1 0 0 0 0 35 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	514.37
Volume:	549.367
LogP:	5.873
LogD:	4.636
LogS:	-5.625
# Rotatable Bonds:	2
TPSA:	72.83
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.407
Synthetic Accessibility Score:	6.219
Fsp3:	0.938
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
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:	-5.13
MDCK Permeability:	1.923140007420443e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.785
30% Bioavailability (F30%):	0.956

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.401
Plasma Protein Binding (PPB):	87.3244400024414%
Volume Distribution (VD):	0.956
Pgp-substrate:	6.933292865753174%

ADMET: Metabolism

CYP1A2-inhibitor:	0.01
CYP1A2-substrate:	0.14
CYP2C19-inhibitor:	0.061
CYP2C19-substrate:	0.838
CYP2C9-inhibitor:	0.267
CYP2C9-substrate:	0.082
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.157
CYP3A4-inhibitor:	0.698
CYP3A4-substrate:	0.502

ADMET: Excretion

Clearance (CL):	6.123
Half-life (T1/2):	0.034

ADMET: Toxicity

hERG Blockers:	0.735
Human Hepatotoxicity (H-HT):	0.68
Drug-inuced Liver Injury (DILI):	0.028
AMES Toxicity:	0.007
Rat Oral Acute Toxicity:	0.863
Maximum Recommended Daily Dose:	0.94
Skin Sensitization:	0.302
Carcinogencity:	0.269
Eye Corrosion:	0.033
Eye Irritation:	0.015
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: NPC2789

Natural Product ID:	NPC2789
*Common Name:**	SFSFDBPTPLSWRM-JWHOUWLXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SFSFDBPTPLSWRM-JWHOUWLXSA-N
Standard InCHI:	InChI=1S/C32H50O5/c1-19(33)36-24-10-11-28(6)20(27(24,4)5)9-12-29(7)21(28)17-23(34)32-22-18-26(2,3)13-15-31(22,25(35)37-32)16-14-30(29,32)8/h20-24,34H,9-18H2,1-8H3/t20-,21-,22-,23+,24+,28+,29-,30+,31+,32-/m1/s1
SMILES:	CC(=O)O[C@H]1CC[C@@]2(C)[C@H](CC[C@]3(C)[C@@H]2C[C@@H]([C@]24[C@@H]5CC(C)(C)CC[C@@]5(CC[C@@]32C)C(=O)O4)O)C1(C)C
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: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
NPO29027	Khaya grandifoliola	Species	Meliaceae	Eukaryota	n.a.	seed	n.a.	PMID[10661881]
NPO15077	Achyranthes bidentata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11430011]
NPO12848	Carpinus cordata	Species	Betulaceae	Eukaryota	stems	n.a.	n.a.	PMID[12350169]
NPO15915	Edgeworthia gardneri	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15387673]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[28294414]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO16642	Astrantia major	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15077	Achyranthes bidentata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16884	Convallaria keiskei	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7987	Tilia vulgaris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16884	Convallaria keiskei	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7987	Tilia vulgaris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26426.1	Cassia javanica subsp. nodosa	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15697	Camellia sasanqua	Species	Theaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15077	Achyranthes bidentata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16642	Astrantia major	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16884	Convallaria keiskei	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15077	Achyranthes bidentata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7987	Tilia vulgaris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO15077	Achyranthes bidentata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO15588	Senecio desfontainei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2038	Myrtus tomentosa	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15915	Edgeworthia gardneri	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12848	Carpinus cordata	Species	Betulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16642	Astrantia major	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16125	Micromonas pusilla	Species	Mamiellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13139	Anatheca montagnei	Species	Solieriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24409	Evasterias troschelii	Species	Asteriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26426.1	Cassia javanica subsp. nodosa	Subspecies	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11994	Thesium humile	Species	Thesiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14807	Arenaria juncea	Species	Scolopacidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8804	Raputia simulans	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO14463	Dirca occidentalis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14936	Agave shawii	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16884	Convallaria keiskei	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5866	Bitis arietans	Species	Viperidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20219	Rhizobium etli	Species	Rhizobiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4589	Sarcotragus spinosulus	Species	Irciniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16025	Werneria decora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27733	Rosa hybrid cultivar	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO820	Grindelia perennis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9479	Ambrosia grayi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16475	Plumbago pulchella	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14313	Pachybasium candidum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2827	Plumeria alba	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15797	Drypetes littoralis	Species	Putranjivaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12490	Lecidea speirodes	Species	Lecideaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15205	Alaria crispa	Species	Alariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11002	Hopea jucunda	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15697	Camellia sasanqua	Species	Theaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11987	Silene inflata	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5047	Evodiopanax innovans	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO16718	Pinna nobilis	Species	Pinnidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11436	Baeomyces roseus	Species	Baeomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15349	Acacia sparsiflora	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16557	Polygala ruwenzoriensis	Species	Polygalaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12293	Euphorbia iberica	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15077	Achyranthes bidentata	Species	Amaranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13442	Eucalyptus regnans	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7987	Tilia vulgaris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13199	Syzygium jambos	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16796	Rumex conglomeratus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29027	Khaya grandifoliola	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11808	Ania latifolia	Species	Orchidaceae	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 NPC2789 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	436
0.1-0.2	3280
0.2-0.3	9059
0.3-0.4	13991
0.4-0.5	6097
0.5-0.6	4735
0.6-0.7	3281
0.7-0.8	1666
0.8-0.85	111
0.85-0.9	30
0.9-0.95	7
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 NPC2789 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	463
0.1-0.2	3521
0.2-0.3	3427
0.3-0.4	1076
0.4-0.5	327
0.5-0.6	218
0.6-0.7	99
0.7-0.8	19
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