NPASS Compound

Structure

NPC256886 OpenBabel06302216132D 37 42 0 0 1 0 0 0 0 0999 V2000 4.4231 0.5662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5100 0.9736 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4064 1.9681 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7006 0.3866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7876 0.7941 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1950 1.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2006 1.6034 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9782 0.2070 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4774 -0.6593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4716 -0.7646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8077 -1.4017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1054 -0.9943 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1062 -1.9295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7593 -2.4301 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9165 -2.3964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7260 -1.9281 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7252 -0.9929 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4578 -1.9913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5347 -0.5246 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5355 -1.5008 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5339 0.4106 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7236 0.8775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9141 0.4092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9149 -0.5260 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0485 -0.0268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3255 0.8676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1294 0.4109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9336 -0.0459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7431 0.4224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5534 -0.0445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5542 -0.9797 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7447 -1.4480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9344 -0.9811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1428 -1.4381 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.3386 -0.9813 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 0.8745 1.2015 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 5 6 1 0 0 0 0 5 7 1 0 0 0 0 5 8 1 0 0 0 0 8 36 1 0 0 0 0 8 9 1 0 0 0 0 8 37 1 1 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 12 11 1 6 0 0 0 12 24 1 0 0 0 0 12 13 1 0 0 0 0 12 36 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 17 24 1 0 0 0 0 17 18 1 6 0 0 0 17 19 1 0 0 0 0 19 35 1 0 0 0 0 19 20 1 1 0 0 0 19 21 1 0 0 0 0 21 22 1 1 0 0 0 21 26 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 26 27 1 0 0 0 0 27 35 2 0 0 0 0 27 28 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	509.24
Volume:	512.874
LogP:	3.528
LogD:	2.671
LogS:	-4.205
# Rotatable Bonds:	3
TPSA:	125.92
# H-Bond Aceptor:	8
# H-Bond Donor:	3
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.531
Synthetic Accessibility Score:	5.43
Fsp3:	0.621
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:	-5.123
MDCK Permeability:	2.3240847440320067e-05
Pgp-inhibitor:	0.801
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.777
20% Bioavailability (F20%):	0.967
30% Bioavailability (F30%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.986
Plasma Protein Binding (PPB):	73.79329681396484%
Volume Distribution (VD):	0.824
Pgp-substrate:	24.065380096435547%

ADMET: Metabolism

CYP1A2-inhibitor:	0.081
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.607
CYP2C19-substrate:	0.893
CYP2C9-inhibitor:	0.488
CYP2C9-substrate:	0.04
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.204
CYP3A4-inhibitor:	0.811
CYP3A4-substrate:	0.934

ADMET: Excretion

Clearance (CL):	6.229
Half-life (T1/2):	0.515

ADMET: Toxicity

hERG Blockers:	0.03
Human Hepatotoxicity (H-HT):	0.672
Drug-inuced Liver Injury (DILI):	0.897
AMES Toxicity:	0.962
Rat Oral Acute Toxicity:	0.955
Maximum Recommended Daily Dose:	0.848
Skin Sensitization:	0.071
Carcinogencity:	0.917
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.857

Download Data

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

Natural Product: NPC256886

Natural Product ID:	NPC256886
*Common Name:**	PWHBDZKTABFTQX-MUQIVTCVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PWHBDZKTABFTQX-MUQIVTCVSA-N
Standard InCHI:	InChI=1S/C29H35NO7/c1-16(31)36-24(2,3)29(35)22(33)15-27(37-29)21(32)11-12-25(4)26(5)17(10-13-28(25,27)34)14-19-18-8-6-7-9-20(18)30-23(19)26/h6-9,17,30,34-35H,10-15H2,1-5H3/t17-,25+,26+,27+,28-,29+/m1/s1
SMILES:	CC(=O)OC(C)(C)[C@@]1(C(=O)C[C@@]2(C(=O)CC[C@@]3(C)[C@@]4(C)[C@H](CC[C@]23O)Cc2c3ccccc3[nH]c42)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0002497] Indoles [CHEMONTID:0004196] 3-alkylindoles

*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
NPO302	Penicillium thiersii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15787428]
NPO3117	Aconitum legendrei	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15125.2	Taxus wallichiana var. wallichiana	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3117	Aconitum legendrei	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3117	Aconitum legendrei	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10069	Chaptalia nutans	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.2	Taxus wallichiana var. wallichiana	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10990	Myristica surinamensis	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9135	Ligularia fauriei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3117	Aconitum legendrei	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2803	Lyonetia clerkella	Species	Lyonetiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO302	Penicillium thiersii	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11104	Diadema antillarum	Species	Diadematidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9915	Pieris brassicae	Species	Pieridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2010	Viburnum ichangense	Species	Adoxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8958	Centella erecta	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8763	Erythrina herbacea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6764	Dianthus japonicus	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16983	Persea obovatifolia	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9566	Abies canadensis	Species	Pinaceae	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 NPC256886 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	362
0.1-0.2	1645
0.2-0.3	4176
0.3-0.4	17276
0.4-0.5	14670
0.5-0.6	3230
0.6-0.7	1162
0.7-0.8	156
0.8-0.85	17
0.85-0.9	3
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 NPC256886 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	248
0.1-0.2	529
0.2-0.3	706
0.3-0.4	2498
0.4-0.5	3570
0.5-0.6	1344
0.6-0.7	248
0.7-0.8	7
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