NPASS Compound

Structure

NPC46375 OpenBabel06302215302D 41 44 0 0 1 0 0 0 0 0999 V2000 11.9926 -4.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.9926 -3.5704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.1266 -3.0704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.2605 -3.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3945 -3.0704 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.3945 -2.0704 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.2605 -1.5704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.1266 -2.0704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.9926 -1.5704 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 8.4810 -2.4772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8118 -1.7340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3118 -0.8680 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.2900 -1.0759 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8173 -1.8385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2295 -1.0295 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4106 -2.7521 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.4161 -2.8566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8283 -2.0476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2350 -1.1340 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8337 -2.1521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2460 -1.3431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2514 -1.4476 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6637 -0.6386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0704 0.2749 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6691 -0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1691 -1.6092 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8090 -1.4013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 -0.4067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7796 -0.9067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 -0.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6456 0.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7796 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9135 0.5933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0475 1.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7796 2.0933 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 1.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3776 0.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5116 -0.9067 0.0000 Br 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 8.5285 -3.5704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.2605 -4.5704 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 1 0 0 0 0 3 4 2 0 0 0 0 4 5 1 0 0 0 0 4 41 1 0 0 0 0 5 6 1 0 0 0 0 5 40 1 6 0 0 0 6 13 1 1 0 0 0 6 7 1 0 0 0 0 6 10 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 25 1 0 0 0 0 25 39 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 33 1 0 0 0 0 28 29 1 6 0 0 0 28 39 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 30 38 1 0 0 0 0 31 32 2 0 0 0 0 31 36 1 0 0 0 0 32 33 1 0 0 0 0 32 35 1 0 0 0 0 33 34 1 6 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	825.85
Volume:	574.445
LogP:	1.339
LogD:	0.71
LogS:	-3.338
# Rotatable Bonds:	9
TPSA:	168.14
# H-Bond Aceptor:	12
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.28
Synthetic Accessibility Score:	6.873
Fsp3:	0.48
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:	-5.434
MDCK Permeability:	1.893696389743127e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.202
Human Intestinal Absorption (HIA):	0.935
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.051
Plasma Protein Binding (PPB):	77.49225616455078%
Volume Distribution (VD):	0.743
Pgp-substrate:	23.604719161987305%

ADMET: Metabolism

CYP1A2-inhibitor:	0.088
CYP1A2-substrate:	0.479
CYP2C19-inhibitor:	0.484
CYP2C19-substrate:	0.347
CYP2C9-inhibitor:	0.24
CYP2C9-substrate:	0.086
CYP2D6-inhibitor:	0.282
CYP2D6-substrate:	0.218
CYP3A4-inhibitor:	0.885
CYP3A4-substrate:	0.295

ADMET: Excretion

Clearance (CL):	1.738
Half-life (T1/2):	0.401

ADMET: Toxicity

hERG Blockers:	0.02
Human Hepatotoxicity (H-HT):	0.854
Drug-inuced Liver Injury (DILI):	0.773
AMES Toxicity:	0.967
Rat Oral Acute Toxicity:	0.932
Maximum Recommended Daily Dose:	0.93
Skin Sensitization:	0.944
Carcinogencity:	0.974
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.986

Download Data

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

Natural Product: NPC46375

Natural Product ID:	NPC46375
*Common Name:**	WHMSDQSUQQPCBG-WIHVIGOGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WHMSDQSUQQPCBG-WIHVIGOGSA-N
Standard InCHI:	InChI=1S/C25H26Br4N4O8/c1-39-18-12(26)5-24(20(35)16(18)28)7-14(32-10-24)22(37)31-9-11(34)3-4-30-23(38)15-8-25(41-33-15)6-13(27)19(40-2)17(29)21(25)36/h5-6,20-21,35-36H,3-4,7-10H2,1-2H3,(H,30,38)(H,31,37)/t20-,21-,24-,25+/m0/s1
SMILES:	COC1=C([C@@H]([C@@]2(C=C1Br)CC(=NC2)C(=O)NCC(=O)CCNC(=O)C1=NO[C@]2(C=C(C(=C([C@@H]2O)Br)OC)Br)C1)O)Br
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0002490] Azolines [CHEMONTID:0002211] Isoxazolines

*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
NPO4817	Briareum excavatum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10096858]
NPO4817	Briareum excavatum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	PMID[10543904]
NPO4817	Briareum excavatum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11277747]
NPO4817	Briareum excavatum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	PMID[11720523]
NPO287	Wrightia javanica	Species	Apocynaceae	Eukaryota	n.a.	leaf	n.a.	PMID[12808258]
NPO4817	Briareum excavatum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9599257]
NPO9047.1	Brassica rapa subsp. oleifera	Subspecies	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO287	Wrightia javanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5510	Lepidium draba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5510	Lepidium draba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9047.1	Brassica rapa subsp. oleifera	Subspecies	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3434	Thymus camphoratus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6901	Lophosoria quadripinnata	Species	Dicksoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5510	Lepidium draba	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8290	Mycena megaspora	Species	Tricholomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6725	Tulipa hybrid	Species	Liliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4191	Thermococcus acidaminovorans	Species	Thermococcaceae	Archaea	n.a.	n.a.	n.a.	Database[UNPD]
NPO8123	Aplysina cavernicola	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2651	Ceroplastes floridensis	Species	Coccidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4817	Briareum excavatum	Species	Briareidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3266	Euryops sulcatus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO287	Wrightia javanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9047.1	Brassica rapa subsp. oleifera	Subspecies	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27875	Fallopia convolvulus	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1594	[enterobacter] aerogenes	Species	Enterobacteriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO1512	Cissampelos fasciculata	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7223	Castela tortuosa	Species	Simaroubaceae	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 NPC46375 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	128
0.1-0.2	1088
0.2-0.3	16005
0.3-0.4	22497
0.4-0.5	2766
0.5-0.6	182
0.6-0.7	14
0.7-0.8	3
0.8-0.85	4
0.85-0.9	6
0.9-0.95	3
0.95-1	1

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 NPC46375 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	91
0.1-0.2	533
0.2-0.3	3630
0.3-0.4	4469
0.4-0.5	414
0.5-0.6	13
0.6-0.7	0
0.7-0.8	0
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