NPASS Compound

Structure

NPC102177 OpenBabel06302215192D 40 47 0 0 1 0 0 0 0 0999 V2000 -2.9842 2.9093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8812 2.5094 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9833 1.5327 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1885 0.9559 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2916 1.3558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1895 2.3325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6341 0.6263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1247 -0.2244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0854 -0.0208 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.6575 0.7295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1669 1.5802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5668 2.4771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5275 2.6808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6307 3.6574 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.7337 4.0573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4307 4.9914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5297 5.1961 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1872 4.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8842 3.5325 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0762 3.3278 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7938 1.3765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2527 2.6915 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8969 0.3999 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.7078 0.8683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5190 0.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5188 -0.5365 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7081 -1.0044 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7081 -1.9405 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0125 -2.5668 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5983 -2.2298 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8970 -0.5361 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.3298 1.8044 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1407 2.2728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1407 3.2088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3295 3.6771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5189 3.2092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5187 2.2727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7078 1.8043 0.0000 N 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 -0.2037 -0.9607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 9 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 7 8 2 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 39 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 11 21 1 0 0 0 0 12 20 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 20 2 0 0 0 0 15 16 1 0 0 0 0 16 17 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 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 31 1 0 0 0 0 23 24 1 0 0 0 0 23 39 1 0 0 0 0 24 38 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 32 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 27 31 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 32 37 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 37 38 1 0 0 0 0 39 40 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	526.16
Volume:	530.541
LogP:	4.282
LogD:	3.159
LogS:	-4.371
# Rotatable Bonds:	3
TPSA:	130.84
# H-Bond Aceptor:	8
# H-Bond Donor:	5
# Rings:	8
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.214
Synthetic Accessibility Score:	4.034
Fsp3:	0.094
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.619
MDCK Permeability:	5.349961156753125e-06
Pgp-inhibitor:	0.015
Pgp-substrate:	0.014
Human Intestinal Absorption (HIA):	0.433
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.313

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.073
Plasma Protein Binding (PPB):	96.8985595703125%
Volume Distribution (VD):	0.408
Pgp-substrate:	1.3870785236358643%

ADMET: Metabolism

CYP1A2-inhibitor:	0.676
CYP1A2-substrate:	0.561
CYP2C19-inhibitor:	0.576
CYP2C19-substrate:	0.525
CYP2C9-inhibitor:	0.764
CYP2C9-substrate:	0.989
CYP2D6-inhibitor:	0.697
CYP2D6-substrate:	0.247
CYP3A4-inhibitor:	0.914
CYP3A4-substrate:	0.868

ADMET: Excretion

Clearance (CL):	1.328
Half-life (T1/2):	0.16

ADMET: Toxicity

hERG Blockers:	0.292
Human Hepatotoxicity (H-HT):	0.802
Drug-inuced Liver Injury (DILI):	0.99
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.568
Maximum Recommended Daily Dose:	0.988
Skin Sensitization:	0.113
Carcinogencity:	0.039
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.901

Download Data

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

Natural Product: NPC102177

Natural Product ID:	NPC102177
*Common Name:**	MTYFENJTEZHZIP-VWLOTQADSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	MTYFENJTEZHZIP-VWLOTQADSA-N
Standard InCHI:	InChI=1S/C32H22N4O4/c37-29-26(20-14-33-22-10-4-1-8-17(20)22)27(21-15-34-23-11-5-2-9-18(21)23)30(38)32(29)28-19(13-25(36-32)31(39)40)16-7-3-6-12-24(16)35-28/h1-12,14-15,25,33-36H,13H2,(H,39,40)/t25-/m0/s1
SMILES:	c1ccc2c(c1)c(c[nH]2)C1=C(c2c[nH]c3ccccc23)C(=O)C2(c3c(C[C@@H](C(=O)O)N2)c2ccccc2[nH]3)C1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11203291
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001140] Harmala alkaloids

*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
NPO2794	Salvia clevelandii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17190465]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22029392]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26081757]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[27169184]
NPO5990	Frangula alnus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9156	Cystophora congesta	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11502	Polystichum aculeatum	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5990	Frangula alnus	Species	Rhamnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10797	Nerine corusca	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23765.1	Cotoneaster salicifolius var. henryanus	Varieties	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5500	Protea eximia	Species	Proteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO929	Corydalis scouleri	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2794	Salvia clevelandii	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2494	Xanthium strumarium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3130	Ainsliaea acerifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14184	Scoliodon walbeehmi	Species	Carcharhinidae	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 NPC102177 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	385
0.1-0.2	2717
0.2-0.3	15682
0.3-0.4	16841
0.4-0.5	2864
0.5-0.6	2163
0.6-0.7	1511
0.7-0.8	506
0.8-0.85	28
0.85-0.9	0
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 NPC102177 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	213
0.1-0.2	574
0.2-0.3	1009
0.3-0.4	2091
0.4-0.5	2511
0.5-0.6	1943
0.6-0.7	699
0.7-0.8	102
0.8-0.85	8
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