NPASS Compound

Structure

NPC109954 OpenBabel06302215422D 37 42 0 0 1 0 0 0 0 0999 V2000 -2.3437 -1.3540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3439 -0.4518 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.1253 -0.0009 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1255 0.9013 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3442 1.3526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5628 0.9016 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5626 -0.0005 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7816 1.3529 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0002 0.9020 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7808 1.3531 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5621 0.9023 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5622 0.0003 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3435 0.4516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7812 -0.4508 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7814 -1.3528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5626 -1.8036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3436 -1.3525 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3438 -2.2547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1254 -2.7058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9065 -2.2544 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6880 -2.7052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5852 -2.6107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9524 -3.4348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8349 -3.6221 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2821 -4.0386 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5007 -3.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9063 -1.3522 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.6878 -1.8030 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9062 -0.4502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1248 0.0009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3434 -0.4505 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.1250 -0.9013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1248 0.9029 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 -3.9069 1.3523 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6881 0.9010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9065 -0.4521 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 7 1 0 0 0 0 3 4 1 0 0 0 0 3 37 1 6 0 0 0 4 5 1 0 0 0 0 4 35 1 6 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 34 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 31 1 0 0 0 0 12 13 1 1 0 0 0 12 14 1 0 0 0 0 14 15 1 6 0 0 0 14 34 1 0 0 0 0 15 16 1 0 0 0 0 17 16 1 1 0 0 0 17 31 1 0 0 0 0 17 32 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 1 0 0 0 20 27 1 0 0 0 0 21 26 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 27 28 1 1 0 0 0 27 29 1 0 0 0 0 27 32 1 0 0 0 0 29 30 1 0 0 0 0 31 30 1 1 0 0 0 32 33 2 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	516.31
Volume:	529.719
LogP:	3.744
LogD:	3.425
LogS:	-4.746
# Rotatable Bonds:	4
TPSA:	98.36
# H-Bond Aceptor:	7
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.522
Synthetic Accessibility Score:	6.438
Fsp3:	0.833
Lipinski Rule-of-5:	Accepted
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:	-5.078
MDCK Permeability:	1.5212511243589688e-05
Pgp-inhibitor:	0.892
Pgp-substrate:	0.131
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.429
30% Bioavailability (F30%):	0.86

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.047
Plasma Protein Binding (PPB):	98.31401824951172%
Volume Distribution (VD):	1.535
Pgp-substrate:	2.240311622619629%

ADMET: Metabolism

CYP1A2-inhibitor:	0.005
CYP1A2-substrate:	0.954
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.79
CYP2C9-inhibitor:	0.186
CYP2C9-substrate:	0.127
CYP2D6-inhibitor:	0.019
CYP2D6-substrate:	0.392
CYP3A4-inhibitor:	0.398
CYP3A4-substrate:	0.645

ADMET: Excretion

Clearance (CL):	12.258
Half-life (T1/2):	0.648

ADMET: Toxicity

hERG Blockers:	0.664
Human Hepatotoxicity (H-HT):	0.457
Drug-inuced Liver Injury (DILI):	0.098
AMES Toxicity:	0.149
Rat Oral Acute Toxicity:	0.859
Maximum Recommended Daily Dose:	0.975
Skin Sensitization:	0.649
Carcinogencity:	0.078
Eye Corrosion:	0.003
Eye Irritation:	0.018
Respiratory Toxicity:	0.96

Download Data

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

Natural Product: NPC109954

Natural Product ID:	NPC109954
*Common Name:**	DFDVWAJDFYYBAC-ZSAFCDTFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DFDVWAJDFYYBAC-ZSAFCDTFSA-N
Standard InCHI:	InChI=1S/C30H44O7/c1-17-26(32)22(34-4)15-25(36-17)37-20-6-9-28(2)19(14-20)5-11-30-12-7-21(18-13-24(31)35-16-18)29(3,27(30)33)10-8-23(28)30/h13,17,19-23,25-26,32H,5-12,14-16H2,1-4H3/t17-,19-,20+,21-,22-,23-,25+,26+,28+,29-,30-/m1/s1
SMILES:	C[C@@H]1[C@@H]([C@@H](C[C@@H](O1)O[C@H]1CC[C@@]2(C)[C@H](CC[C@@]34CC[C@H](C5=CC(=O)OC5)[C@@](C)(CC[C@H]23)C4=O)C1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	131701096
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl compounds

*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
NPO26266	Isodon japonicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1039/C39730000707]
NPO1071	Parerythropodium fulvum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[11277760]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	leaves	Niigata City, Niigata Province, Japan	2000-Nov	PMID[15730243]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	leaves	n.a.	n.a.	PMID[16933868]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17253842]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	stems and twigs	n.a.	n.a.	PMID[17595134]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	stems and twigs	Niigata City, Niigata Province, Japan	2001-NOV	PMID[17595134]
NPO26266	Isodon japonicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18491868]
NPO3936	Malva sylvestris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19731587]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29693393]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	Leaves; Stems	n.a.	n.a.	PMID[9214727]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3664	Mesembryanthemum anatomicum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13325	Plantago lanceolata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3936	Malva sylvestris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6520	Myrica multiflora	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2747	Hypericum triquetrifolium	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14048	Cryptotaenia japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2518	Crinum kirkii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13325	Plantago lanceolata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6520	Myrica multiflora	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3936	Malva sylvestris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3664	Mesembryanthemum anatomicum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14048	Cryptotaenia japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2747	Hypericum triquetrifolium	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14048	Cryptotaenia japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6520	Myrica multiflora	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20132	Scutellaria seleriana	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2747	Hypericum triquetrifolium	Species	Hypericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO715	Teucrium pestalozzae	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5980	Eria subsessilis	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15583	Tripodanthus acutifolius	Species	Loranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3146	Ammodendron conollyi	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8472	Knightia deplanchei	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1071	Parerythropodium fulvum	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO2518	Crinum kirkii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3936	Malva sylvestris	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO351	Cirsium dipsacolepis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5197	Streptomyces eurythermus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4253	Viguiera annua	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6776	Trifolium apertum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1308	Veronica pectinata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3664	Mesembryanthemum anatomicum	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2361	Aconitum brevicalcaratum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8585	Verpa digitaliformis	Species	Morchellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14048	Cryptotaenia japonica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10021	Nerium oleander	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6377	Cocculus diversifolius	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4082	Ophiarthrum elegans	Species	Ophiocomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7097	Rhynchosporium orthosporum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2342	Cytisus scoparius	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12987	Rhododendron farrerae	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8840	Ptilidium ciliare	Species	Ptilidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18054	Curvularia coicis	Species	Pleosporaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6974	Solanum racemigerum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26266	Isodon japonicus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5591	Fucus spiralis	Species	Fucaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13325	Plantago lanceolata	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1607	Croton rhamnifolius	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 NPC109954 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	263
0.1-0.2	1569
0.2-0.3	4483
0.3-0.4	8035
0.4-0.5	12473
0.5-0.6	7726
0.6-0.7	4813
0.7-0.8	2310
0.8-0.85	560
0.85-0.9	459
0.9-0.95	6
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 NPC109954 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	239
0.1-0.2	1774
0.2-0.3	3730
0.3-0.4	2225
0.4-0.5	687
0.5-0.6	315
0.6-0.7	144
0.7-0.8	19
0.8-0.85	15
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