NPASS Compound

Structure

CID202722 OpenBabel06191715592D 28 32 0 0 1 0 0 0 0 0999 V2000 4.1587 -0.5179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0612 2.9286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0266 2.6453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2914 -0.9516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4848 -2.1243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3888 -1.7035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3585 -1.7035 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4848 1.4922 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2693 0.9222 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6046 -0.7581 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5215 2.1441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4912 2.1441 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4822 -0.4174 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5743 -0.7581 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2997 0.9222 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2219 1.2219 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4387 0.5513 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5039 0.8093 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.7909 1.2219 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3683 2.1187 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4604 1.7780 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9697 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -3.7131 0.9222 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6262 3.0535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4755 1.8940 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0064 0.6519 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9729 1.3606 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 4 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 6 10 1 0 0 0 0 7 14 1 0 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 22 1 0 0 0 0 10 23 1 0 0 0 0 11 12 1 0 0 0 0 12 2 1 1 0 0 0 12 19 1 0 0 0 0 13 4 1 6 0 0 0 13 14 1 0 0 0 0 13 17 1 0 0 0 0 14 22 1 1 0 0 0 15 16 1 0 0 0 0 15 23 1 6 0 0 0 16 11 1 1 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 17 28 1 6 0 0 0 18 21 1 6 0 0 0 18 22 1 0 0 0 0 19 24 2 0 0 0 0 19 27 1 0 0 0 0 20 21 1 0 0 0 0 20 25 2 0 0 0 0 20 28 1 0 0 0 0 21 3 1 1 0 0 0 21 26 1 0 0 0 0 22 23 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	391.24
Volume:	395.961
LogP:	3.662
LogD:	3.443
LogS:	-4.559
# Rotatable Bonds:	2
TPSA:	76.07
# H-Bond Aceptor:	6
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.728
Synthetic Accessibility Score:	5.625
Fsp3:	0.909
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.849
MDCK Permeability:	7.933748565847054e-05
Pgp-inhibitor:	0.81
Pgp-substrate:	0.005
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.026
30% Bioavailability (F30%):	0.863

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.294
Plasma Protein Binding (PPB):	60.405487060546875%
Volume Distribution (VD):	1.661
Pgp-substrate:	42.952484130859375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.031
CYP1A2-substrate:	0.091
CYP2C19-inhibitor:	0.133
CYP2C19-substrate:	0.764
CYP2C9-inhibitor:	0.235
CYP2C9-substrate:	0.067
CYP2D6-inhibitor:	0.206
CYP2D6-substrate:	0.208
CYP3A4-inhibitor:	0.885
CYP3A4-substrate:	0.914

ADMET: Excretion

Clearance (CL):	8.482
Half-life (T1/2):	0.099

ADMET: Toxicity

hERG Blockers:	0.319
Human Hepatotoxicity (H-HT):	0.787
Drug-inuced Liver Injury (DILI):	0.57
AMES Toxicity:	0.01
Rat Oral Acute Toxicity:	0.301
Maximum Recommended Daily Dose:	0.269
Skin Sensitization:	0.343
Carcinogencity:	0.174
Eye Corrosion:	0.014
Eye Irritation:	0.015
Respiratory Toxicity:	0.82

Download Data

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

Natural Product: NPC202722

Natural Product ID:	NPC202722
*Common Name:**	SVSUKQDSRBZWNP-MYKAZKENSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SVSUKQDSRBZWNP-MYKAZKENSA-N
Standard InCHI:	InChI=1S/C22H33NO5/c1-4-13-14-7-5-6-10-23-15(16-11-12(2)19(24)27-16)8-9-22(14,23)18-17(13)28-20(25)21(18,3)26/h12-18,26H,4-11H2,1-3H3/p+1/t12-,13+,14+,15-,16-,17+,18-,21-,22+/m0/s1
SMILES:	CC[C@@H]1[C@H]2CCCC[NH+]3[C@@H](CC[C@]23[C@H]2[C@@H]1OC(=O)[C@@]2(C)O)[C@@H]1C[C@H](C)C(=O)O1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3237634
PubChem CID:	90655426
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0003427] Stemona alkaloids [CHEMONTID:0003914] Stemoamide-type alkaloids [CHEMONTID:0003429] Stichoneurine-type 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
NPO10055	Stichoneuron caudatum	Species	Stemonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24606395]
NPO10055	Stichoneuron caudatum	Species	Stemonaceae	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Individual Protein	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT204	Individual Protein	Acetylcholinesterase	Homo sapiens	IC50	>	100000.0	nM	PMID[518162]

☑ 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 NPC202722 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	300
0.1-0.2	4864
0.2-0.3	20140
0.3-0.4	13971
0.4-0.5	2926
0.5-0.6	445
0.6-0.7	38
0.7-0.8	7
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	5

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC471846
1.0	High Similarity	NPC39041
1.0	High Similarity	NPC471845
1.0	High Similarity	NPC241294
0.8288	Intermediate Similarity	NPC471844
0.7568	Intermediate Similarity	NPC471843
0.7241	Intermediate Similarity	NPC233274
0.7241	Intermediate Similarity	NPC287638
0.7241	Intermediate Similarity	NPC194750
0.7132	Intermediate Similarity	NPC474371
0.7045	Intermediate Similarity	NPC215507
0.6891	Remote Similarity	NPC265094
0.6887	Remote Similarity	NPC216090
0.6875	Remote Similarity	NPC11379
0.6847	Remote Similarity	NPC52533
0.6814	Remote Similarity	NPC476019
0.669	Remote Similarity	NPC956
0.6637	Remote Similarity	NPC203170
0.6615	Remote Similarity	NPC230849
0.6525	Remote Similarity	NPC88943
0.6519	Remote Similarity	NPC173173
0.6491	Remote Similarity	NPC322966
0.6466	Remote Similarity	NPC473477
0.6462	Remote Similarity	NPC174463
0.6397	Remote Similarity	NPC212106
0.6389	Remote Similarity	NPC233108
0.6283	Remote Similarity	NPC277918
0.6271	Remote Similarity	NPC469998
0.6232	Remote Similarity	NPC470539
0.621	Remote Similarity	NPC97336
0.6202	Remote Similarity	NPC469466
0.6197	Remote Similarity	NPC474210
0.6115	Remote Similarity	NPC309249
0.609	Remote Similarity	NPC235625
0.6087	Remote Similarity	NPC476501
0.6087	Remote Similarity	NPC476951
0.6063	Remote Similarity	NPC271562
0.6061	Remote Similarity	NPC470538
0.6043	Remote Similarity	NPC476497
0.6042	Remote Similarity	NPC45813
0.5986	Remote Similarity	NPC133089
0.5984	Remote Similarity	NPC160066
0.5954	Remote Similarity	NPC76660
0.5954	Remote Similarity	NPC276995
0.5942	Remote Similarity	NPC326386
0.5942	Remote Similarity	NPC471087
0.5942	Remote Similarity	NPC477985
0.5909	Remote Similarity	NPC63191
0.5909	Remote Similarity	NPC471202
0.5887	Remote Similarity	NPC220234
0.5882	Remote Similarity	NPC88190
0.5859	Remote Similarity	NPC168890
0.5857	Remote Similarity	NPC280903
0.5839	Remote Similarity	NPC23963
0.5821	Remote Similarity	NPC476502
0.5816	Remote Similarity	NPC471086
0.5814	Remote Similarity	NPC176756
0.5775	Remote Similarity	NPC476967
0.5769	Remote Similarity	NPC15413
0.5769	Remote Similarity	NPC220773
0.5769	Remote Similarity	NPC167044
0.5769	Remote Similarity	NPC278693
0.5755	Remote Similarity	NPC293550
0.5755	Remote Similarity	NPC111162
0.5755	Remote Similarity	NPC477989
0.5755	Remote Similarity	NPC477990
0.5755	Remote Similarity	NPC323168
0.5748	Remote Similarity	NPC227622
0.5745	Remote Similarity	NPC470537
0.5736	Remote Similarity	NPC236644
0.5735	Remote Similarity	NPC476952
0.5734	Remote Similarity	NPC307165
0.5725	Remote Similarity	NPC217041
0.5714	Remote Similarity	NPC469999
0.5692	Remote Similarity	NPC137453
0.5682	Remote Similarity	NPC182185
0.5667	Remote Similarity	NPC292345
0.5662	Remote Similarity	NPC209734
0.5652	Remote Similarity	NPC208118
0.5652	Remote Similarity	NPC99905
0.5652	Remote Similarity	NPC96080
0.5649	Remote Similarity	NPC15440
0.5649	Remote Similarity	NPC264958
0.5649	Remote Similarity	NPC185590
0.5639	Remote Similarity	NPC30911
0.5639	Remote Similarity	NPC316984
0.5635	Remote Similarity	NPC211087
0.5635	Remote Similarity	NPC474952
0.563	Remote Similarity	NPC92139
0.5625	Remote Similarity	NPC5864
0.5625	Remote Similarity	NPC124554
0.5625	Remote Similarity	NPC301148
0.5625	Remote Similarity	NPC292803
0.562	Remote Similarity	NPC475887
0.5615	Remote Similarity	NPC469441
0.5615	Remote Similarity	NPC41674
0.5615	Remote Similarity	NPC228311
0.5612	Remote Similarity	NPC477238
0.5612	Remote Similarity	NPC238323

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 NPC202722 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	207
0.1-0.2	2528
0.2-0.3	4534
0.3-0.4	1481
0.4-0.5	346
0.5-0.6	53
0.6-0.7	1
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
0.669	Remote Similarity	NPD5193	Discontinued
0.6063	Remote Similarity	NPD8307	Discontinued
0.6063	Remote Similarity	NPD8140	Approved
0.5985	Remote Similarity	NPD7915	Approved
0.5985	Remote Similarity	NPD7916	Approved
0.5965	Remote Similarity	NPD883	Phase 2
0.5965	Remote Similarity	NPD882	Phase 2
0.5938	Remote Similarity	NPD1829	Clinical (unspecified phase)
0.5938	Remote Similarity	NPD1827	Clinical (unspecified phase)
0.5938	Remote Similarity	NPD1828	Approved
0.5935	Remote Similarity	NPD3714	Approved
0.5935	Remote Similarity	NPD3713	Approved
0.5935	Remote Similarity	NPD3715	Approved
0.5827	Remote Similarity	NPD8276	Approved
0.5827	Remote Similarity	NPD8275	Approved
0.5802	Remote Similarity	NPD8087	Discontinued
0.5766	Remote Similarity	NPD8346	Approved
0.5766	Remote Similarity	NPD8345	Approved
0.5766	Remote Similarity	NPD8347	Approved
0.5748	Remote Similarity	NPD8086	Approved
0.5748	Remote Similarity	NPD8084	Approved
0.5748	Remote Similarity	NPD8085	Approved
0.5748	Remote Similarity	NPD8083	Approved
0.5748	Remote Similarity	NPD8138	Approved
0.5748	Remote Similarity	NPD8082	Approved
0.5748	Remote Similarity	NPD8139	Approved
0.5736	Remote Similarity	NPD8393	Approved
0.5736	Remote Similarity	NPD6920	Discontinued
0.5667	Remote Similarity	NPD4264	Clinical (unspecified phase)
0.5667	Remote Similarity	NPD618	Clinical (unspecified phase)
0.5659	Remote Similarity	NPD8081	Approved
0.5639	Remote Similarity	NPD2204	Approved

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