NPASS Compound

Structure

NPC68899 OpenBabel06302215142D 44 47 0 0 1 0 0 0 0 0999 V2000 -7.7942 -0.5000 0.0000 C 0 0 0 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 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 N 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 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 C 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 -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 -2.5981 -0.5000 0.0000 C 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 -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 -0.8660 1.5000 0.0000 O 0 0 0 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 2 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 1.7321 -0.0000 0.0000 C 0 0 1 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 0.3660 -1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -1.3660 0.0000 C 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 2.5981 -0.5000 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 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 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 -5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -2.0000 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 44 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 10 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 12 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 1 0 0 0 0 15 25 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 43 1 0 0 0 0 17 23 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 28 27 1 1 0 0 0 28 29 1 0 0 0 0 28 35 1 0 0 0 0 29 30 1 0 0 0 0 29 42 1 1 0 0 0 30 31 1 0 0 0 0 30 38 1 1 0 0 0 31 32 1 0 0 0 0 31 36 1 6 0 0 0 32 33 1 0 0 0 0 32 34 1 0 0 0 0 32 35 1 0 0 0 0 36 37 1 0 0 0 0 38 39 1 0 0 0 0 39 40 2 0 0 0 0 39 41 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	612.23
Volume:	600.191
LogP:	4.108
LogD:	2.426
LogS:	-4.056
# Rotatable Bonds:	10
TPSA:	200.01
# H-Bond Aceptor:	13
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.233
Synthetic Accessibility Score:	4.448
Fsp3:	0.387
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:	-5.505
MDCK Permeability:	8.547779543732759e-06
Pgp-inhibitor:	0.316
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.071
20% Bioavailability (F20%):	0.011
30% Bioavailability (F30%):	0.982

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.021
Plasma Protein Binding (PPB):	85.14000701904297%
Volume Distribution (VD):	0.719
Pgp-substrate:	8.772191047668457%

ADMET: Metabolism

CYP1A2-inhibitor:	0.061
CYP1A2-substrate:	0.092
CYP2C19-inhibitor:	0.041
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.337
CYP2C9-substrate:	0.087
CYP2D6-inhibitor:	0.222
CYP2D6-substrate:	0.147
CYP3A4-inhibitor:	0.129
CYP3A4-substrate:	0.069

ADMET: Excretion

Clearance (CL):	3.727
Half-life (T1/2):	0.294

ADMET: Toxicity

hERG Blockers:	0.028
Human Hepatotoxicity (H-HT):	0.92
Drug-inuced Liver Injury (DILI):	0.98
AMES Toxicity:	0.244
Rat Oral Acute Toxicity:	0.469
Maximum Recommended Daily Dose:	0.016
Skin Sensitization:	0.231
Carcinogencity:	0.381
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.004

Download Data

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

Natural Product: NPC68899

Natural Product ID:	NPC68899
*Common Name:**	YJQPYGGHQPGBLI-PTSPBZQHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YJQPYGGHQPGBLI-PTSPBZQHSA-N
Standard InCHI:	InChI=1S/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29+/m0/s1
SMILES:	CC(=CCc1cc(ccc1O)C(=O)Nc1c(c2ccc(c(C)c2oc1=O)O[C@H]1[C@H]([C@H]([C@@H](C(C)(C)O1)OC)OC(=N)O)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	73896877
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0001743] Coumarin 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
NPO3333	Aglaia gigantea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17880174]
NPO1526	Ratibida latipalearis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1800631]
NPO6655	Streptomyces niveus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19762445]
NPO2575	Psorothamnus fremontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26469557]
NPO2575	Psorothamnus fremontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2681536]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16616	Juniperus virginiana	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9603	Croton sparsiflorus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16616	Juniperus virginiana	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9603	Croton sparsiflorus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9020	Eriostemon fitzgeraldii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16616	Juniperus virginiana	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12481	Croton californicus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8547	Petasites niveus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7365	Clibadium pentaneuron	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19843	Rohdea yunnanensis	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12309	Malva crispa	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3900	Phellinus xeranticus	Species	Hymenochaetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11362	Givotia madagascariensis	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12535	Solanum toxicarium	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7883	Albugo candida	Species	Albuginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2575	Psorothamnus fremontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24849	Rhinella paracnemis	Species	Bufonidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12950	Squalus suckleyi	Species	Squalidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2805	Distolasterias nipon	Species	Asteriidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17065	Streptomyces griseoflavus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO3202	0lina erumpens	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO729	Espeletia marcana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6655	Streptomyces niveus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO9227	Xylaria berteri	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2502	Lupinus mexicanus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1937	Andropogon nardus	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5219	Dendrobium rotundatum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3333	Aglaia gigantea	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6787	Neoalsomitra integrifolia	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24652	Toxicodendron succedaneum	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9320	Weddellina squamulosa	Species	Podostemaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8416	Picrorhiza kurrooa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18350	Culcitium canescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9603	Croton sparsiflorus	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10867	Graphis elongata	Species	Aclididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9937	Piptolepis leptospermoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11355	Homarus americanus	Species	Nephropidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1526	Ratibida latipalearis	Species	Asteraceae	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 NPC68899 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	356
0.1-0.2	1726
0.2-0.3	5525
0.3-0.4	11130
0.4-0.5	6774
0.5-0.6	9911
0.6-0.7	6771
0.7-0.8	490
0.8-0.85	1
0.85-0.9	6
0.9-0.95	1
0.95-1	6

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 NPC68899 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	236
0.1-0.2	633
0.2-0.3	1168
0.3-0.4	2118
0.4-0.5	2789
0.5-0.6	1729
0.6-0.7	455
0.7-0.8	19
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	3

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