NPASS Compound

Structure

NPC63959 OpenBabel06302215282D 42 42 0 0 0 0 0 0 0 0999 V2000 -10.3923 -22.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 -22.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -22.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -21.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -20.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -19.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -19.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -18.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -17.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -16.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -16.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -15.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -14.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -13.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -13.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -4.0000 0.0000 C 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 2.5981 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 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 0.0000 2.0000 0.0000 C 0 0 0 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 0.5000 0.0000 C 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 -1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 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 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 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 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 39 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 42 1 0 0 0 0 38 39 1 0 0 0 0 38 40 1 0 0 0 0 40 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	586.5
Volume:	679.226
LogP:	13.349
LogD:	4.94
LogS:	-7.579
# Rotatable Bonds:	31
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.055
Synthetic Accessibility Score:	2.534
Fsp3:	0.763
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.425
MDCK Permeability:	3.6764668038813397e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.161
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	103.75272369384766%
Volume Distribution (VD):	6.806
Pgp-substrate:	0.4953688085079193%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.131
CYP2C19-inhibitor:	0.127
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.023
CYP2C9-substrate:	0.991
CYP2D6-inhibitor:	0.144
CYP2D6-substrate:	0.127
CYP3A4-inhibitor:	0.16
CYP3A4-substrate:	0.023

ADMET: Excretion

Clearance (CL):	4.679
Half-life (T1/2):	0.04

ADMET: Toxicity

hERG Blockers:	0.946
Human Hepatotoxicity (H-HT):	0.013
Drug-inuced Liver Injury (DILI):	0.37
AMES Toxicity:	0.014
Rat Oral Acute Toxicity:	0.012
Maximum Recommended Daily Dose:	0.082
Skin Sensitization:	0.991
Carcinogencity:	0.024
Eye Corrosion:	0.25
Eye Irritation:	0.909
Respiratory Toxicity:	0.493

Download Data

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

Natural Product: NPC63959

Natural Product ID:	NPC63959
*Common Name:**	PIGLOISSVVAGBD-NHQGMKOOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PIGLOISSVVAGBD-NHQGMKOOSA-N
Standard InCHI:	InChI=1S/C38H66O4/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-33-42-38(40)32-30-35-29-31-36(39)37(34-35)41-2/h29-32,34,39H,3-28,33H2,1-2H3/b32-30+
SMILES:	CCCCCCCCCCCCCCCCCCCCCCCCCCCCOC(=O)/C=C/c1ccc(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5743442
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000476] Cinnamic acids and derivatives [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives [CHEMONTID:0000059] Coumaric acids and derivatives

*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
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12502328]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[16792421]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17488128]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[17489632]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	PMID[18484536]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	stem bark	Mukono, Uganda	2005-JUN	PMID[19008110]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19534474]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19836230]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20337486]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21116437]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	whole plants	Panshi, Jilin Province, China	2009-JUN	PMID[21534540]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[21534540]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	roots	n.a.	n.a.	PMID[24660966]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25453801]
NPO6701	Cinnamomum camphora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25612070]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26702644]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28383891]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	Roots	n.a.	n.a.	PMID[29148766]
NPO8159	Digenea simplex	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31117523]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31184480]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7775984]
NPO6701	Cinnamomum camphora	Species	Lauraceae	Eukaryota	n.a.	stem	n.a.	Database[Article]
NPO6701	Cinnamomum camphora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8159	Digenea simplex	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13272	Ulva lactuca	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18641	Radix euphorbiae pekinensis	Species	Lymnaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13272	Ulva lactuca	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6701	Cinnamomum camphora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8159	Digenea simplex	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13272	Ulva lactuca	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6701	Cinnamomum camphora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21462	Lannea grandis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11421	Arnebia euchroma	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9209	Rhizomnium magnifolium	Species	Mniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO299	Euphorbia ebracteolata	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8159	Digenea simplex	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6701	Cinnamomum camphora	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8526	Erythrina abyssinica	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16205	Euphorbia fischeriana	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11300	Eucalyptus coccifera	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13272	Ulva lactuca	Species	Ulvaceae	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 NPC63959 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	249
0.1-0.2	1352
0.2-0.3	4266
0.3-0.4	10477
0.4-0.5	7823
0.5-0.6	4806
0.6-0.7	9935
0.7-0.8	3213
0.8-0.85	405
0.85-0.9	136
0.9-0.95	24
0.95-1	11

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 NPC63959 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	228
0.1-0.2	878
0.2-0.3	1759
0.3-0.4	2666
0.4-0.5	1775
0.5-0.6	1046
0.6-0.7	697
0.7-0.8	95
0.8-0.85	4
0.85-0.9	2
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