NPASS Compound

Structure

NPC93202 OpenBabel06302215422D 45 47 0 0 1 0 0 0 0 0999 V2000 -3.6529 4.0722 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7560 3.6299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9246 4.1855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6906 2.6320 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5221 2.0765 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.1394 1.1526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1586 1.3477 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1394 0.1526 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5221 -0.7713 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2292 -1.4784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1531 -1.8611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1531 -1.8611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0770 -1.4784 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7841 -0.7713 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -8.1667 0.1526 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.1475 -0.0425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4690 -0.9894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8096 -1.7413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1311 -2.6882 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.1118 -2.8833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7712 -2.1315 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.4498 -1.1845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.7520 -2.3265 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -10.4333 -3.8302 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.4717 -3.4400 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -8.1667 1.1526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7841 2.0765 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -7.0770 2.7836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1531 3.1663 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3482 4.1470 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1531 3.1663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9580 4.1470 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2292 2.7836 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1475 1.3477 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6325 -2.3099 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6906 -1.3269 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7560 -2.3247 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7937 -0.8846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9623 -1.4401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0654 -0.9979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7661 -1.5534 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6629 -1.1111 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7283 -0.1133 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8969 0.4423 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 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 5 4 1 1 0 0 0 5 6 1 0 0 0 0 5 33 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 9 36 1 6 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 13 14 2 3 0 0 0 13 35 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 6 0 0 0 15 26 1 0 0 0 0 16 17 1 0 0 0 0 17 22 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 19 25 1 0 0 0 0 20 21 2 0 0 0 0 20 24 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 26 27 2 3 0 0 0 26 34 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 1 0 0 0 29 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 36 37 1 1 0 0 0 36 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 40 45 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 43 44 2 0 0 0 0 44 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	658.22
Volume:	653.26
LogP:	5.693
LogD:	4.633
LogS:	-4.498
# Rotatable Bonds:	7
TPSA:	131.36
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.331
Synthetic Accessibility Score:	5.168
Fsp3:	0.441
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:	-4.823
MDCK Permeability:	1.181045354314847e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.012
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.21
30% Bioavailability (F30%):	0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.502
Plasma Protein Binding (PPB):	98.67452239990234%
Volume Distribution (VD):	0.336
Pgp-substrate:	2.52309250831604%

ADMET: Metabolism

CYP1A2-inhibitor:	0.111
CYP1A2-substrate:	0.077
CYP2C19-inhibitor:	0.72
CYP2C19-substrate:	0.13
CYP2C9-inhibitor:	0.894
CYP2C9-substrate:	0.944
CYP2D6-inhibitor:	0.282
CYP2D6-substrate:	0.103
CYP3A4-inhibitor:	0.929
CYP3A4-substrate:	0.794

ADMET: Excretion

Clearance (CL):	3.066
Half-life (T1/2):	0.208

ADMET: Toxicity

hERG Blockers:	0.064
Human Hepatotoxicity (H-HT):	0.973
Drug-inuced Liver Injury (DILI):	0.942
AMES Toxicity:	0.041
Rat Oral Acute Toxicity:	0.294
Maximum Recommended Daily Dose:	0.589
Skin Sensitization:	0.194
Carcinogencity:	0.139
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.03

Download Data

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

Natural Product: NPC93202

Natural Product ID:	NPC93202
*Common Name:**	ISTUVLRTAHDXQL-DQHTXJPTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ISTUVLRTAHDXQL-DQHTXJPTSA-N
Standard InCHI:	InChI=1S/C34H40Cl2N2O7/c1-20(2)15-29-34(43)44-28(21(3)13-14-23-9-6-5-7-10-23)11-8-12-30(39)38-27(32(41)37-19-22(4)33(42)45-29)18-24-16-25(35)31(40)26(36)17-24/h5-10,12-14,16-17,20-22,27-29,40H,11,15,18-19H2,1-4H3,(H,37,41)(H,38,39)/b12-8+,14-13+/t21-,22-,27-,28+,29+/m1/s1
SMILES:	CC(C)C[C@H]1C(=O)O[C@@H](C/C=C/C(=N[C@H](Cc2cc(c(c(c2)Cl)O)Cl)C(=NC[C@@H](C)C(=O)O1)O)O)[C@H](C)/C=C/c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10746911
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0002010] Hybrid peptides

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24476550]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO8945	Grevillea robusta	Species	Proteaceae	Eukaryota	leaves	n.a.	n.a.	PMID[17243726]
NPO4541	Capnella lacertiliensis	Species	Nephtheidae	Eukaryota	n.a.	n.a.	n.a.	PMID[12608844]
NPO3613	Eriobotrya deflexa	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11473413]
NPO18618	Neurolaena lobata	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	DOI[10.1021/jo00416a020]
NPO8811	Cytisus prolifer	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1969	Streptomyces pilosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO19804	Lycopodium saururus	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28833	Eleutherococcus sieboldianus	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC93202 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	181
0.1-0.2	989
0.2-0.3	5109
0.3-0.4	13150
0.4-0.5	13795
0.5-0.6	8750
0.6-0.7	667
0.7-0.8	41
0.8-0.85	3
0.85-0.9	8
0.9-0.95	4
0.95-1	0

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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 NPC93202 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	124
0.1-0.2	514
0.2-0.3	1022
0.3-0.4	2204
0.4-0.5	3189
0.5-0.6	1848
0.6-0.7	238
0.7-0.8	9
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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