NPASS Compound

Structure

NPC118170 OpenBabel06302215202D 39 43 0 0 1 0 0 0 0 0999 V2000 -1.3134 0.8681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3167 0.9485 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1563 1.9356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4445 2.7350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3479 3.1637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3471 3.1235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3471 4.1235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2132 4.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2132 5.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0792 4.1235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9452 4.6235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0792 3.1235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8223 2.4543 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.8005 2.6622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4696 1.9191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4641 2.0236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8709 1.1101 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.1277 0.4409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1277 -0.5591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2617 -1.0591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3957 -0.5591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3957 0.4409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2617 0.9409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4156 1.5408 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.4211 1.6453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2132 2.6235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.7476 1.7783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6962 2.0949 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8281 0.7815 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4361 -0.1385 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6615 -0.7709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0902 -1.6744 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6817 -0.9709 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6415 -1.9701 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7212 -0.6927 0.0000 C 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 1.5664 -0.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7519 0.9022 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4811 4.6235 0.0000 O 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 2 36 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 26 1 0 0 0 0 7 8 1 0 0 0 0 7 39 1 6 0 0 0 8 9 2 0 0 0 0 8 10 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 12 26 1 0 0 0 0 13 14 1 0 0 0 0 13 24 1 0 0 0 0 14 15 1 0 0 0 0 15 23 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 23 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 38 1 0 0 0 0 26 27 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 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 35 36 2 0 0 0 0 35 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	528.26
Volume:	556.189
LogP:	3.48
LogD:	2.937
LogS:	-4.193
# Rotatable Bonds:	2
TPSA:	116.33
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	5
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.309
Synthetic Accessibility Score:	5.863
Fsp3:	0.438
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.009
MDCK Permeability:	1.3152016435924452e-05
Pgp-inhibitor:	0.885
Pgp-substrate:	0.965
Human Intestinal Absorption (HIA):	0.083
20% Bioavailability (F20%):	0.204
30% Bioavailability (F30%):	0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.191
Plasma Protein Binding (PPB):	91.0591812133789%
Volume Distribution (VD):	0.68
Pgp-substrate:	4.284546375274658%

ADMET: Metabolism

CYP1A2-inhibitor:	0.065
CYP1A2-substrate:	0.195
CYP2C19-inhibitor:	0.501
CYP2C19-substrate:	0.348
CYP2C9-inhibitor:	0.521
CYP2C9-substrate:	0.344
CYP2D6-inhibitor:	0.069
CYP2D6-substrate:	0.124
CYP3A4-inhibitor:	0.935
CYP3A4-substrate:	0.246

ADMET: Excretion

Clearance (CL):	6.256
Half-life (T1/2):	0.267

ADMET: Toxicity

hERG Blockers:	0.065
Human Hepatotoxicity (H-HT):	0.819
Drug-inuced Liver Injury (DILI):	0.528
AMES Toxicity:	0.074
Rat Oral Acute Toxicity:	0.908
Maximum Recommended Daily Dose:	0.96
Skin Sensitization:	0.151
Carcinogencity:	0.127
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.98

Download Data

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

Natural Product: NPC118170

Natural Product ID:	NPC118170
*Common Name:**	PTPJKVDJLHYTML-XANHDBJGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PTPJKVDJLHYTML-XANHDBJGSA-N
Standard InCHI:	InChI=1S/C32H36N2O5/c1-17-8-7-10-23-30(38)20(4)19(3)28-25(15-21-16-33-24-11-6-5-9-22(21)24)34-31(39)32(23,28)27(36)13-12-26(35)29(37)18(2)14-17/h5-7,9-11,14,16-17,19,23,25,28,30,33,38H,4,8,12-13,15H2,1-3H3,(H,34,39)/b10-7+,18-14+/t17-,19+,23-,25-,28-,30+,32+/m0/s1
SMILES:	C[C@H]1C/C=C/[C@H]2[C@@H](C(=C)[C@@H](C)[C@H]3[C@H](Cc4c[nH]c5ccccc45)N=C([C@@]23C(=O)CCC(=O)C(=O)/C(=C/1)/C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	23259926
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001819] Isoindoles and derivatives [CHEMONTID:0002496] Isoindolines [CHEMONTID:0001820] Isoindolones

*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
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12357398]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12483566]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15497948]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15921417]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16209910]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499339]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16872138]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16904330]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17125234]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17827664]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19246197]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	Ginkgo biloba	n.a.	n.a.	PMID[19246197]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19427327]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20225834]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20814854]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	isolated from the leaves of Viguiera robusta	n.a.	n.a.	PMID[21548578]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	mycelium	n.a.	PMID[21548578]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21548578]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21640594]
NPO997	Peltodon longipes	Species	Lamiaceae	Eukaryota	roots	Santa Maria, South Brazil	2007-Dec	PMID[21775156]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21854043]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22112725]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22593034]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23072467]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	Xichang of Sichuan Province, China	n.a.	PMID[26125976]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26343828]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5066072]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7116505]
NPO2853	Eschweilera coriacea	Species	Lecythidaceae	Eukaryota	bark	Suriname rainforest	n.a.	PMID[9677272]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[CiteXplore Id]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3809	Eucalyptus cladocalyx	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5665	Ulva pertusa	Species	Ulvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23741	Aspergillus violaceus	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1920	Podocarpus elongata	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3809	Eucalyptus cladocalyx	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6621	Salvadora persica	Species	Salvadoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24171	Chaetomium globosum	Species	Chaetomiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2853	Eschweilera coriacea	Species	Lecythidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO997	Peltodon longipes	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5665	Ulva pertusa	Species	Ulvaceae	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 NPC118170 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	318
0.1-0.2	1448
0.2-0.3	5610
0.3-0.4	21532
0.4-0.5	9047
0.5-0.6	2287
0.6-0.7	1984
0.7-0.8	433
0.8-0.85	5
0.85-0.9	18
0.9-0.95	13
0.95-1	2

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 NPC118170 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	193
0.1-0.2	540
0.2-0.3	593
0.3-0.4	1966
0.4-0.5	2959
0.5-0.6	2082
0.6-0.7	729
0.7-0.8	88
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