NPASS Compound

Structure

NPC137880 OpenBabel06302215112D 56 61 0 0 1 0 0 0 0 0999 V2000 1.6771 -1.9365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6771 -0.9683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5156 -0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5156 0.4841 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3541 0.9683 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1927 0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0312 0.9683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0312 1.9365 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.8697 1.4524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8697 2.4206 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.6267 1.8169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5707 2.0324 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9908 2.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9591 2.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5707 3.7771 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6267 3.9926 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4113 4.9366 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8697 3.3889 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.4152 2.5889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9951 1.7165 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5405 0.9165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1204 0.0441 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5060 0.9889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0312 3.8730 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1927 3.3889 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1927 2.4206 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3541 1.9365 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3541 2.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5156 2.4206 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6771 1.9365 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6771 0.9683 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8385 1.4524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8385 0.4841 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8385 -0.4841 0.0000 C 0 0 2 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 0.8385 1.4524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6771 1.9365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.9048 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8385 2.4206 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8385 3.3889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6771 3.8730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.8730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5156 4.3571 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6771 4.8413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6771 5.8095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8385 4.3571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3541 3.8730 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3541 4.8413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1927 5.3254 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5156 5.3254 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0312 5.8095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8697 6.2937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8697 7.2619 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7083 5.8095 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3541 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 31 1 0 0 0 0 4 5 1 0 0 0 0 4 56 1 1 0 0 0 5 6 1 1 0 0 0 5 27 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 26 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 1 0 0 0 10 18 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 0 0 0 0 13 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 24 25 1 0 0 0 0 24 52 1 6 0 0 0 25 26 1 0 0 0 0 25 48 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 44 1 1 0 0 0 30 31 1 0 0 0 0 30 40 1 1 0 0 0 31 32 1 1 0 0 0 31 33 1 0 0 0 0 33 35 1 0 0 0 0 33 34 1 0 0 0 0 33 36 1 6 0 0 0 34 2 1 1 0 0 0 34 35 1 0 0 0 0 36 37 2 0 0 0 0 36 38 1 0 0 0 0 38 39 1 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 43 1 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 47 1 0 0 0 0 48 49 1 0 0 0 0 49 50 2 0 0 0 0 49 51 1 0 0 0 0 52 53 1 0 0 0 0 53 54 2 0 0 0 0 53 55 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	786.35
Volume:	774.478
LogP:	2.577
LogD:	1.37
LogS:	-4.645
# Rotatable Bonds:	13
TPSA:	199.79
# H-Bond Aceptor:	15
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.17
Synthetic Accessibility Score:	6.319
Fsp3:	0.707
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:	-5.342
MDCK Permeability:	0.00015951847308315337
Pgp-inhibitor:	0.999
Pgp-substrate:	0.445
Human Intestinal Absorption (HIA):	0.968
20% Bioavailability (F20%):	0.987
30% Bioavailability (F30%):	0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.263
Plasma Protein Binding (PPB):	38.145992279052734%
Volume Distribution (VD):	1.644
Pgp-substrate:	31.749969482421875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.007
CYP1A2-substrate:	0.031
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.071
CYP2C9-inhibitor:	0.008
CYP2C9-substrate:	0.002
CYP2D6-inhibitor:	0.159
CYP2D6-substrate:	0.052
CYP3A4-inhibitor:	0.621
CYP3A4-substrate:	0.406

ADMET: Excretion

Clearance (CL):	2.406
Half-life (T1/2):	0.64

ADMET: Toxicity

hERG Blockers:	0.212
Human Hepatotoxicity (H-HT):	0.977
Drug-inuced Liver Injury (DILI):	0.8
AMES Toxicity:	0.427
Rat Oral Acute Toxicity:	0.865
Maximum Recommended Daily Dose:	0.328
Skin Sensitization:	0.145
Carcinogencity:	0.046
Eye Corrosion:	0.003
Eye Irritation:	0.023
Respiratory Toxicity:	0.945

Download Data

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

Natural Product: NPC137880

Natural Product ID:	NPC137880
*Common Name:**	PGUFYOHQERCXID-BGKFFRIMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PGUFYOHQERCXID-BGKFFRIMSA-N
Standard InCHI:	InChI=1S/C41H54O15/c1-19-17-40(48)28-15-16-36(9)27-14-13-20(2)51-21(3)39(27,18-50-22(4)42)32(53-24(6)44)29(52-23(5)43)30(36)37(28,10)33(54-25(7)45)34(55-26(8)46)38(40,11)41(31(19)56-41)35(47)49-12/h13-14,21,27-34,48H,1-2,15-18H2,3-12H3/t21-,27+,28-,29+,30+,31-,32+,33-,34+,36+,37+,38-,39-,40-,41+/m1/s1
SMILES:	C=C1C[C@]2([C@@H]3CC[C@@]4(C)[C@@H]5C=CC(=C)O[C@H](C)[C@@]5(COC(=O)C)[C@H]([C@H]([C@@H]4[C@@]3(C)[C@@H]([C@@H]([C@@]2(C)[C@]2([C@@H]1O2)C(=O)OC)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101470671
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002967] Hexacarboxylic 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
NPO15284	Periconia byssoides	Species	Periconiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21391658]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	heartwood	n.a.	n.a.	PMID[23743282]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9525107]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO18726	Spatholobus roxburghii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19405	Hovea acutifolia	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3857	Perezia multiflora	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18960	Lophanthera lactescens	Species	Malpighiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17971	Coryphantha vivipara	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6577	Spongia equina	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15284	Periconia byssoides	Species	Periconiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17836	Ostrea edulis	Species	Ostreidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14405	Randia siamensis	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18117	Dalbergia odorifera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16663	Malus orientalis	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26037	Linaria genistifolia	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18888	Goniothalamus sesquipedalis	Species	Annonaceae	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 NPC137880 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	301
0.1-0.2	1681
0.2-0.3	4265
0.3-0.4	7069
0.4-0.5	13626
0.5-0.6	9205
0.6-0.7	4794
0.7-0.8	1722
0.8-0.85	32
0.85-0.9	2
0.9-0.95	0
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 NPC137880 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	279
0.1-0.2	1679
0.2-0.3	3612
0.3-0.4	2243
0.4-0.5	872
0.5-0.6	339
0.6-0.7	115
0.7-0.8	11
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