NPASS Compound

Structure

NPC11558 OpenBabel06302216032D 30 32 0 0 1 0 0 0 0 0999 V2000 0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 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 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 N 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 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0519 2.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8440 1.2128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5871 0.5437 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5382 0.8527 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7461 1.8309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0029 3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.0519 3.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7429 4.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 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 -2.5981 -0.5000 0.0000 O 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 0.0000 0.0000 0.0000 C 0 0 2 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 1.7321 -0.0000 0.0000 C 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 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 3 2 1 6 0 0 0 3 4 1 0 0 0 0 3 22 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 19 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 16 1 0 0 0 0 8 9 1 0 0 0 0 8 18 1 1 0 0 0 9 14 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 1 0 0 0 23 24 2 0 0 0 0 23 27 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	322.17
Volume:	335.449
LogP:	2.81
LogD:	2.883
LogS:	-4.186
# Rotatable Bonds:	2
TPSA:	45.33
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	6
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.682
Synthetic Accessibility Score:	5.281
Fsp3:	0.45
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.897
MDCK Permeability:	1.9249609977123328e-05
Pgp-inhibitor:	0.044
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.757
20% Bioavailability (F20%):	0.588
30% Bioavailability (F30%):	0.574

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.77
Plasma Protein Binding (PPB):	79.44840240478516%
Volume Distribution (VD):	1.88
Pgp-substrate:	9.996498107910156%

ADMET: Metabolism

CYP1A2-inhibitor:	0.601
CYP1A2-substrate:	0.801
CYP2C19-inhibitor:	0.383
CYP2C19-substrate:	0.582
CYP2C9-inhibitor:	0.187
CYP2C9-substrate:	0.909
CYP2D6-inhibitor:	0.35
CYP2D6-substrate:	0.902
CYP3A4-inhibitor:	0.898
CYP3A4-substrate:	0.765

ADMET: Excretion

Clearance (CL):	8.544
Half-life (T1/2):	0.257

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.164
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.156
Rat Oral Acute Toxicity:	0.758
Maximum Recommended Daily Dose:	0.994
Skin Sensitization:	0.918
Carcinogencity:	0.902
Eye Corrosion:	0.03
Eye Irritation:	0.025
Respiratory Toxicity:	0.988

Download Data

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

Natural Product: NPC11558

Natural Product ID:	NPC11558
*Common Name:**	BSZMATVWFZYBEG-XNOOYMFHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BSZMATVWFZYBEG-XNOOYMFHSA-N
Standard InCHI:	InChI=1S/C22H28N2O6/c1-4-14-12-24(19(25)11-15(14)16(13-29-2)20(26)30-3)10-9-22(28)17-7-5-6-8-18(17)23-21(22)27/h5-8,13-15,28H,4,9-12H2,1-3H3,(H,23,27)/b16-13-/t14-,15-,22-/m0/s1
SMILES:	CC[C@H]1CN(CC[C@@]2(c3ccccc3N=C2O)O)C(=O)C[C@@H]1/C(=C/OC)/C(=O)OC
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
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27359163]
NPO1603	Monostroma nitidum	Species	Monostromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19160	Klasea quinquefolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1603	Monostroma nitidum	Species	Monostromataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4468	Cuspidaria pterocarpa	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9282	Stereocaulon colensoi	Species	Stereocaulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO907	Dictyostelium purpureum	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14694	Sickingia williamsii	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO22126	Penicillium funiculosum	Species	Trichocomaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6849	Lomatia arborescens	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10315	Cestrum parqui	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11596	Lomatia ilicifolia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10499	Haplopappus paucidentatus	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 NPC11558 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	182
0.1-0.2	898
0.2-0.3	3616
0.3-0.4	11345
0.4-0.5	17026
0.5-0.6	7984
0.6-0.7	1574
0.7-0.8	48
0.8-0.85	22
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 NPC11558 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	125
0.1-0.2	424
0.2-0.3	701
0.3-0.4	1256
0.4-0.5	2568
0.5-0.6	3337
0.6-0.7	734
0.7-0.8	5
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