NPASS Compound

Structure

NPC184080 OpenBabel06302215522D 82 88 0 0 1 0 0 0 0 0999 V2000 2.5689 5.4382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5689 4.4494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7126 3.9551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 3.9551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 2.9663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2815 2.4719 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2815 1.4831 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1378 0.9888 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9941 1.4831 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.9941 2.4719 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.1378 2.9663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8504 2.9663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8504 3.9551 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9941 3.4607 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1378 3.9551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1378 4.9438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9941 5.4382 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2815 5.4382 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2815 6.4270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 6.9213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5689 6.4270 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7126 6.9213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7126 7.9101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5689 8.4045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 7.9101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5689 9.3933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7126 9.8876 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8563 8.4045 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8337 4.0584 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.0393 5.0256 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.1830 5.5199 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0796 6.5033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1764 6.9055 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4482 4.8583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.9426 5.4277 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4953 3.3236 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4625 3.5292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7680 4.4696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.1241 2.7944 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8185 1.8540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4802 1.1192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.4473 1.3248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.7529 2.2652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.0912 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7067 0.4944 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7067 -0.4944 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5629 -0.9888 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.5629 -1.9775 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7067 -2.4719 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.8504 -1.9775 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9941 -2.4719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9941 -3.4607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8504 -0.9888 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7067 -3.4607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4192 -2.4719 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.4192 -0.4944 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1378 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2815 -0.4944 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2815 -1.4831 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4252 -1.9775 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5689 -1.4831 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5689 -0.4944 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7126 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8563 -0.4944 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7126 -1.9775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 -2.9663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1378 -1.9775 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4252 0.9888 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5689 1.4831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5689 2.4719 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7126 0.9888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8563 1.4831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8563 1.4831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7126 0.9888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7126 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8563 -0.4944 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 -0.8563 -1.4831 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7126 -1.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5689 -0.4944 0.0000 O 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 4 5 1 0 0 0 0 6 5 1 1 0 0 0 6 7 1 0 0 0 0 6 11 1 0 0 0 0 7 8 1 0 0 0 0 7 69 1 6 0 0 0 8 9 1 0 0 0 0 8 57 1 1 0 0 0 9 10 1 0 0 0 0 9 45 1 6 0 0 0 10 11 1 0 0 0 0 10 12 1 6 0 0 0 12 13 1 0 0 0 0 13 34 1 0 0 0 0 13 14 1 1 0 0 0 13 29 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 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 28 1 0 0 0 0 24 25 1 0 0 0 0 24 26 1 0 0 0 0 26 27 1 0 0 0 0 29 30 1 0 0 0 0 29 36 1 6 0 0 0 30 31 1 0 0 0 0 30 35 1 1 0 0 0 31 32 1 6 0 0 0 31 34 1 0 0 0 0 32 33 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 44 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 46 45 1 1 0 0 0 46 47 1 0 0 0 0 46 53 1 0 0 0 0 47 48 1 0 0 0 0 47 56 1 6 0 0 0 48 49 1 0 0 0 0 48 55 1 1 0 0 0 49 50 1 0 0 0 0 49 54 1 6 0 0 0 50 51 1 1 0 0 0 50 53 1 0 0 0 0 51 52 1 0 0 0 0 58 57 1 1 0 0 0 58 59 1 0 0 0 0 58 65 1 0 0 0 0 59 60 1 0 0 0 0 59 68 1 6 0 0 0 60 61 1 0 0 0 0 60 67 1 1 0 0 0 61 62 1 0 0 0 0 61 66 1 6 0 0 0 62 63 1 1 0 0 0 62 65 1 0 0 0 0 63 64 1 0 0 0 0 69 70 1 0 0 0 0 70 71 2 0 0 0 0 70 72 1 0 0 0 0 72 73 2 0 0 0 0 73 74 1 0 0 0 0 74 79 2 0 0 0 0 74 75 1 0 0 0 0 75 76 2 0 0 0 0 76 77 1 0 0 0 0 77 78 2 0 0 0 0 77 82 1 0 0 0 0 78 79 1 0 0 0 0 78 80 1 0 0 0 0 80 81 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	110.07
Volume:	124.589
LogP:	0.458
LogD:	0.606
LogS:	-0.172
# Rotatable Bonds:	1
TPSA:	20.23
# H-Bond Aceptor:	1
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	1

MedChem Properties

QED Drug-Likeness Score:	0.538
Synthetic Accessibility Score:	3.185
Fsp3:	0.429
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.361
MDCK Permeability:	3.095431748079136e-05
Pgp-inhibitor:	0.003
Pgp-substrate:	0.036
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.984
Plasma Protein Binding (PPB):	36.88288116455078%
Volume Distribution (VD):	0.845
Pgp-substrate:	62.91986846923828%

ADMET: Metabolism

CYP1A2-inhibitor:	0.152
CYP1A2-substrate:	0.392
CYP2C19-inhibitor:	0.031
CYP2C19-substrate:	0.76
CYP2C9-inhibitor:	0.02
CYP2C9-substrate:	0.343
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.863
CYP3A4-inhibitor:	0.006
CYP3A4-substrate:	0.248

ADMET: Excretion

Clearance (CL):	2.505
Half-life (T1/2):	0.865

ADMET: Toxicity

hERG Blockers:	0.031
Human Hepatotoxicity (H-HT):	0.446
Drug-inuced Liver Injury (DILI):	0.044
AMES Toxicity:	0.25
Rat Oral Acute Toxicity:	0.817
Maximum Recommended Daily Dose:	0.842
Skin Sensitization:	0.96
Carcinogencity:	0.659
Eye Corrosion:	0.826
Eye Irritation:	0.989
Respiratory Toxicity:	0.937

Download Data

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

Natural Product: NPC184080

Natural Product ID:	NPC184080
*Common Name:**	PCSSAXAXMOBEOT-KUDGPSRDSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PCSSAXAXMOBEOT-KUDGPSRDSA-N
Standard InCHI:	InChI=1S/C53H64O29/c1-24(57)72-22-35-45(77-37(61)16-12-26-10-14-29(59)31(18-26)71-3)46(78-50-43(67)41(65)38(62)32(19-54)74-50)47(79-51-44(68)42(66)39(63)33(20-55)75-51)52(76-35)82-53(23-73-36(60)15-11-25-9-13-28(58)30(17-25)70-2)48(40(64)34(21-56)81-53)80-49(69)27-7-5-4-6-8-27/h4-18,32-35,38-48,50-52,54-56,58-59,62-68H,19-23H2,1-3H3/b15-11+,16-12+/t32-,33-,34-,35-,38-,39-,40-,41+,42+,43-,44-,45-,46+,47-,48+,50+,51+,52-,53+/m1/s1
SMILES:	CC(=O)OC[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@]1(COC(=O)/C=C/c2ccc(c(c2)OC)O)[C@H]([C@@H]([C@@H](CO)O1)O)OC(=O)c1ccccc1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC(=O)/C=C/c1ccc(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10079963
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24617303]
NPO27081	Clavularia inflata	Species	Clavulariidae	Eukaryota	n.a.	Formosan soft coral	n.a.	PMID[11520220]
NPO27808	Cremanthodium discoideum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10579856]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	flower	n.a.	DOI[10.3390/70200245]
NPO28295	Foeniculum vulgare	Species	Apiaceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1016/S0031-9422(00)94055-X]
NPO28521	Delphinium vestitum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27081	Clavularia inflata	Species	Clavulariidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27934	Mezilaurus synandra	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20099	Petalostylis labicheoides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27846	Aeodes ulvoidea	Species	Halymeniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC184080 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	354
0.1-0.2	1448
0.2-0.3	3236
0.3-0.4	7467
0.4-0.5	9800
0.5-0.6	7199
0.6-0.7	8466
0.7-0.8	4049
0.8-0.85	541
0.85-0.9	122
0.9-0.95	14
0.95-1	1

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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 NPC184080 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	297
0.1-0.2	802
0.2-0.3	1731
0.3-0.4	2717
0.4-0.5	2135
0.5-0.6	1060
0.6-0.7	349
0.7-0.8	47
0.8-0.85	12
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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