NPASS Compound

Structure

NPC127113 OpenBabel06302215172D 50 54 0 0 1 0 0 0 0 0999 V2000 -3.2425 -3.0547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6654 -3.8490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0647 -4.7459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0412 -4.8485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6183 -4.0542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2189 -3.1573 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7960 -2.3630 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -5.5947 -4.1569 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1718 -3.3625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1482 -3.4652 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.7253 -2.6709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3260 -1.7739 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.9031 -0.9796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5037 -0.0827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8795 -1.0823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3704 -1.9325 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -10.3308 -1.7284 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.4334 -0.7520 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.2837 -1.2429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1340 -0.7520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1340 0.2299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9843 0.7208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2837 0.7208 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.4334 0.2299 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.5831 0.7208 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.2837 1.7026 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -12.9843 -1.2429 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -9.5365 -0.3526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5476 -4.3621 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4405 -5.7455 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -1.6889 -3.7463 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2896 -2.8494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8667 -2.0551 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4673 -1.1582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4855 -0.9529 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1425 -1.6825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0394 -1.2832 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.9368 -0.3068 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9764 -0.1026 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5535 0.6917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1542 1.5886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1778 1.6912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2216 2.5882 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3993 0.8969 0.0000 C 0 0 2 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 -0.5771 -0.7943 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3758 0.9996 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 1.7313 2.3829 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -2.0444 -0.3639 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1118 -4.5406 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 2 31 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 30 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 29 1 6 0 0 0 11 12 1 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 28 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 24 1 0 0 0 0 18 19 1 6 0 0 0 18 28 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 24 1 0 0 0 0 23 26 1 1 0 0 0 24 25 1 6 0 0 0 31 32 1 0 0 0 0 31 50 1 6 0 0 0 32 33 1 0 0 0 0 33 34 2 3 0 0 0 34 49 1 0 0 0 0 35 34 1 6 0 0 0 35 36 1 0 0 0 0 35 39 1 0 0 0 0 36 37 2 0 0 0 0 37 38 1 0 0 0 0 38 39 1 0 0 0 0 39 45 1 0 0 0 0 39 40 1 1 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 41 48 1 0 0 0 0 42 43 2 0 0 0 0 42 44 1 0 0 0 0 44 45 1 0 0 0 0 44 47 1 6 0 0 0 45 46 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1079.67
Volume:	694.738
LogP:	1.944
LogD:	0.345
LogS:	-4.065
# Rotatable Bonds:	12
TPSA:	225.67
# H-Bond Aceptor:	15
# H-Bond Donor:	6
# Rings:	5
# Heavy Atoms:	21

MedChem Properties

QED Drug-Likeness Score:	0.186
Synthetic Accessibility Score:	6.572
Fsp3:	0.448
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.733
MDCK Permeability:	4.473703302210197e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.059
Human Intestinal Absorption (HIA):	0.938
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.202
Plasma Protein Binding (PPB):	98.9476547241211%
Volume Distribution (VD):	0.995
Pgp-substrate:	5.934906959533691%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.213
CYP2C19-inhibitor:	0.594
CYP2C19-substrate:	0.246
CYP2C9-inhibitor:	0.528
CYP2C9-substrate:	0.039
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.135
CYP3A4-inhibitor:	0.944
CYP3A4-substrate:	0.316

ADMET: Excretion

Clearance (CL):	0.393
Half-life (T1/2):	0.034

ADMET: Toxicity

hERG Blockers:	0.12
Human Hepatotoxicity (H-HT):	0.816
Drug-inuced Liver Injury (DILI):	0.419
AMES Toxicity:	0.936
Rat Oral Acute Toxicity:	0.11
Maximum Recommended Daily Dose:	0.966
Skin Sensitization:	0.375
Carcinogencity:	0.54
Eye Corrosion:	0.003
Eye Irritation:	0.003
Respiratory Toxicity:	0.962

Download Data

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

Natural Product: NPC127113

Natural Product ID:	NPC127113
*Common Name:**	JGGJQFOWZXXRKT-WVTAVEGASA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JGGJQFOWZXXRKT-WVTAVEGASA-N
Standard InCHI:	InChI=1S/C29H26Br6N4O11/c30-13-1-10(18(41)8-37-26(46)12-7-38-50-29(12)4-16(33)22(43)20(35)25(29)45)2-14(31)23(13)48-9-11(40)6-36-27(47)17-5-28(49-39-17)3-15(32)21(42)19(34)24(28)44/h1-4,7,11-12,18-20,24-25,40-41,44-45H,5-6,8-9H2,(H,36,47)(H,37,46)/t11-,12-,18+,19-,20-,24+,25+,28-,29-/m1/s1
SMILES:	c1c(cc(c(c1Br)OC[C@@H](CNC(=O)C1=NO[C@]2(C=C(C(=O)[C@H]([C@@H]2O)Br)Br)C1)O)Br)[C@H](CN=C([C@H]1C=NO[C@@]21C=C(C(=O)[C@H]([C@@H]2O)Br)Br)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0002341] Phenol ethers

*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
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[11170659]
NPO27012	Laurencia pannosa	Species	Rhodomelaceae	Eukaryota	n.a.	Malaysian	n.a.	PMID[11374951]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	leaves	n.a.	n.a.	PMID[12502329]
NPO27072	Monochaetum vulcanicum	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15165161]
NPO17223	Agelas oroides	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	PMID[32072810]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27773	Rhododendron ovatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7497	Guatteria blepharophylla	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26895	Baccharis bigelovii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11140	Coprinopsis cinerea	Species	Psathyrellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27012	Laurencia pannosa	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22488	Leptosphaeria oraemaris	Species	Leptosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27648	Cereus aethiops	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27569	Archangelica officinalis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27688	Aeonium goochiae	Species	Crassulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20208	Rhinogobius brunneus	Species	Gobiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27707	Soja hispida	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17223	Agelas oroides	Species	Agelasidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16500	Byssochlamys spectabilis	Species	Thermoascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27072	Monochaetum vulcanicum	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27323	Cestrum nocturnum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27773	Rhododendron ovatum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27262	Dryopteris inaequalis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27191	Schistochila appendiculata	Species	Schistochilaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27725	Artemisia vestita	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27740	Alcantara ekmaniana	n.a.	n.a.	n.a.	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 NPC127113 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	337
0.1-0.2	1672
0.2-0.3	7042
0.3-0.4	11398
0.4-0.5	12393
0.5-0.6	9582
0.6-0.7	245
0.7-0.8	12
0.8-0.85	8
0.85-0.9	5
0.9-0.95	3
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 NPC127113 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	179
0.1-0.2	652
0.2-0.3	1408
0.3-0.4	2725
0.4-0.5	3031
0.5-0.6	1116
0.6-0.7	39
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