Structure

Physi-Chem Properties

Molecular Weight:  400.14
Volume:  377.491
LogP:  -0.583
LogD:  0.29
LogS:  -0.837
# Rotatable Bonds:  9
TPSA:  166.14
# H-Bond Aceptor:  10
# H-Bond Donor:  6
# Rings:  2
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.215
Synthetic Accessibility Score:  3.854
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.971
MDCK Permeability:  0.00022473403078038245
Pgp-inhibitor:  0.001
Pgp-substrate:  0.988
Human Intestinal Absorption (HIA):  0.863
20% Bioavailability (F20%):  0.632
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.527
Plasma Protein Binding (PPB):  45.407127380371094%
Volume Distribution (VD):  0.295
Pgp-substrate:  62.553585052490234%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.024
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.068
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.439
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.152
CYP3A4-inhibitor:  0.018
CYP3A4-substrate:  0.034

ADMET: Excretion

Clearance (CL):  1.57
Half-life (T1/2):  0.73

ADMET: Toxicity

hERG Blockers:  0.06
Human Hepatotoxicity (H-HT):  0.056
Drug-inuced Liver Injury (DILI):  0.013
AMES Toxicity:  0.303
Rat Oral Acute Toxicity:  0.333
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.382
Carcinogencity:  0.214
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.034

Download Data

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

  Natural Product: NPC5209

Natural Product ID:  NPC5209
Common Name*:   SXYIRMFQILZOAM-DAWBJHCGSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SXYIRMFQILZOAM-DAWBJHCGSA-N
Standard InCHI:  InChI=1S/C16H26O5/c1-9-5-6-12-10(2)13(17-4)18-14-16(12)11(9)7-8-15(3,19-14)20-21-16/h9-14H,5-8H2,1-4H3/t9-,10-,11+,12+,13?,14-,15+,16-/m1/s1
SMILES:  C[C@@H]1CC[C@H]2[C@@H](C)C(OC)O[C@H]3[C@]42[C@H]1CC[C@@](C)(O3)OO4
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3349376
PubChem CID:   45006102
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002440] Artemisinins

*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
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. flower n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. leaf n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. stem n.a. DOI[10.1007/s11418-006-0112-9]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. PMID[6387056]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26589 Artemisia annua L. Strain Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10506 Artemisia apiacea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26589 Artemisia annua L. Strain Asteraceae 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 7.5 nM PMID[531474]

☑ 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 NPC5209 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC29005
1.0 High Similarity NPC51956
0.9275 High Similarity NPC209666
0.9275 High Similarity NPC31046
0.9275 High Similarity NPC200167
0.9275 High Similarity NPC53868
0.8442 Intermediate Similarity NPC30102
0.8442 Intermediate Similarity NPC67158
0.8442 Intermediate Similarity NPC128816
0.8421 Intermediate Similarity NPC260977
0.8421 Intermediate Similarity NPC30443
0.8421 Intermediate Similarity NPC285480
0.8421 Intermediate Similarity NPC45256
0.8026 Intermediate Similarity NPC177343
0.7821 Intermediate Similarity NPC60568
0.7733 Intermediate Similarity NPC166250
0.76 Intermediate Similarity NPC123122
0.7564 Intermediate Similarity NPC272841
0.7531 Intermediate Similarity NPC241959
0.75 Intermediate Similarity NPC308489
0.7375 Intermediate Similarity NPC471216
0.7375 Intermediate Similarity NPC471217
0.7349 Intermediate Similarity NPC290612
0.7333 Intermediate Similarity NPC471879
0.7308 Intermediate Similarity NPC107963
0.7284 Intermediate Similarity NPC71541
0.7262 Intermediate Similarity NPC471410
0.7262 Intermediate Similarity NPC471411
0.7209 Intermediate Similarity NPC131466
0.7176 Intermediate Similarity NPC140446
0.7176 Intermediate Similarity NPC43912
0.7143 Intermediate Similarity NPC476718
0.7125 Intermediate Similarity NPC477577
0.7111 Intermediate Similarity NPC148872
0.7108 Intermediate Similarity NPC470070
0.7073 Intermediate Similarity NPC476494
0.7059 Intermediate Similarity NPC107603
0.7059 Intermediate Similarity NPC268633
0.7045 Intermediate Similarity NPC229801
0.7045 Intermediate Similarity NPC210759
0.7045 Intermediate Similarity NPC307167
0.7037 Intermediate Similarity NPC170595
0.7024 Intermediate Similarity NPC474156
0.7011 Intermediate Similarity NPC82955
0.7 Intermediate Similarity NPC132998
0.6977 Remote Similarity NPC472396
0.6966 Remote Similarity NPC323231
0.6966 Remote Similarity NPC224003
0.6966 Remote Similarity NPC470623
0.6966 Remote Similarity NPC171741
0.6966 Remote Similarity NPC18724
0.6951 Remote Similarity NPC186588
0.6951 Remote Similarity NPC475456
0.6933 Remote Similarity NPC477754
0.6933 Remote Similarity NPC477758
0.6933 Remote Similarity NPC477761
0.6933 Remote Similarity NPC477760
0.6933 Remote Similarity NPC477759
0.6933 Remote Similarity NPC179823
0.6932 Remote Similarity NPC261990
0.6932 Remote Similarity NPC474249
0.6932 Remote Similarity NPC279329
0.6932 Remote Similarity NPC65550
0.6897 Remote Similarity NPC281004
0.6889 Remote Similarity NPC309866
0.6889 Remote Similarity NPC305418
0.6889 Remote Similarity NPC45959
0.6889 Remote Similarity NPC252253
0.6889 Remote Similarity NPC253611
0.6889 Remote Similarity NPC267238
0.6889 Remote Similarity NPC471373
0.6889 Remote Similarity NPC148593
0.6889 Remote Similarity NPC77717
0.6875 Remote Similarity NPC279575
0.686 Remote Similarity NPC474008
0.6854 Remote Similarity NPC289361
0.6854 Remote Similarity NPC36372
0.6854 Remote Similarity NPC59006
0.6854 Remote Similarity NPC473830
0.6854 Remote Similarity NPC293609
0.6854 Remote Similarity NPC204881
0.6824 Remote Similarity NPC166279
0.6824 Remote Similarity NPC18953
0.6818 Remote Similarity NPC102725
0.6818 Remote Similarity NPC473472
0.6813 Remote Similarity NPC106701
0.6813 Remote Similarity NPC471425
0.6813 Remote Similarity NPC471424
0.6813 Remote Similarity NPC471429
0.6813 Remote Similarity NPC94582
0.6813 Remote Similarity NPC92196
0.6813 Remote Similarity NPC189575
0.6813 Remote Similarity NPC205129
0.6813 Remote Similarity NPC57964
0.6813 Remote Similarity NPC477494
0.68 Remote Similarity NPC477764
0.68 Remote Similarity NPC477752
0.68 Remote Similarity NPC477751
0.68 Remote Similarity NPC477756
0.679 Remote Similarity NPC476719
0.6786 Remote Similarity NPC470611
0.6778 Remote Similarity NPC144790
0.6778 Remote Similarity NPC149400
0.6778 Remote Similarity NPC137004
0.6778 Remote Similarity NPC167644
0.6778 Remote Similarity NPC473726
0.6778 Remote Similarity NPC88962
0.6778 Remote Similarity NPC277774
0.6778 Remote Similarity NPC311246
0.6778 Remote Similarity NPC172838
0.6742 Remote Similarity NPC473542
0.6742 Remote Similarity NPC223143
0.6739 Remote Similarity NPC304011
0.6739 Remote Similarity NPC238796
0.6739 Remote Similarity NPC237071
0.6739 Remote Similarity NPC142264
0.6739 Remote Similarity NPC203434
0.6739 Remote Similarity NPC476510
0.6739 Remote Similarity NPC139271
0.6709 Remote Similarity NPC470659
0.6709 Remote Similarity NPC470660
0.6706 Remote Similarity NPC213737
0.6706 Remote Similarity NPC475820
0.6706 Remote Similarity NPC474284
0.6706 Remote Similarity NPC474346
0.6706 Remote Similarity NPC474253
0.6705 Remote Similarity NPC470872
0.6705 Remote Similarity NPC221993
0.6703 Remote Similarity NPC178949
0.6703 Remote Similarity NPC291547
0.6703 Remote Similarity NPC312678
0.6703 Remote Similarity NPC175
0.6703 Remote Similarity NPC174024
0.6703 Remote Similarity NPC477224
0.6703 Remote Similarity NPC473851
0.6703 Remote Similarity NPC113500
0.6703 Remote Similarity NPC131693
0.6703 Remote Similarity NPC253268
0.6703 Remote Similarity NPC473503
0.6703 Remote Similarity NPC30687
0.6703 Remote Similarity NPC24960
0.6703 Remote Similarity NPC179859
0.6703 Remote Similarity NPC473774
0.6703 Remote Similarity NPC475436
0.6703 Remote Similarity NPC151214
0.6703 Remote Similarity NPC191915
0.6703 Remote Similarity NPC96736
0.6703 Remote Similarity NPC3538
0.6667 Remote Similarity NPC476668
0.6667 Remote Similarity NPC470836
0.6667 Remote Similarity NPC149966
0.6667 Remote Similarity NPC470028
0.6667 Remote Similarity NPC477222
0.6667 Remote Similarity NPC473637
0.6667 Remote Similarity NPC477223
0.6667 Remote Similarity NPC471368
0.6667 Remote Similarity NPC5632
0.6667 Remote Similarity NPC233649
0.663 Remote Similarity NPC473067
0.663 Remote Similarity NPC473065
0.663 Remote Similarity NPC474399
0.663 Remote Similarity NPC469710
0.663 Remote Similarity NPC473064
0.6629 Remote Similarity NPC20822
0.6627 Remote Similarity NPC477287
0.6596 Remote Similarity NPC471374
0.6596 Remote Similarity NPC471375
0.6596 Remote Similarity NPC209798
0.6593 Remote Similarity NPC249204
0.6593 Remote Similarity NPC325828
0.6593 Remote Similarity NPC477547
0.6593 Remote Similarity NPC177834
0.6593 Remote Similarity NPC250393
0.6593 Remote Similarity NPC35164
0.6593 Remote Similarity NPC297348
0.6593 Remote Similarity NPC234352
0.6593 Remote Similarity NPC477451
0.6593 Remote Similarity NPC476669
0.6593 Remote Similarity NPC48339
0.6593 Remote Similarity NPC141769
0.6591 Remote Similarity NPC110365
0.6591 Remote Similarity NPC161928
0.6591 Remote Similarity NPC210658
0.6591 Remote Similarity NPC45833
0.6591 Remote Similarity NPC62202
0.6591 Remote Similarity NPC213658
0.6588 Remote Similarity NPC296734
0.6588 Remote Similarity NPC208912
0.6588 Remote Similarity NPC2096
0.6585 Remote Similarity NPC188793
0.6559 Remote Similarity NPC473287
0.6559 Remote Similarity NPC472989
0.6559 Remote Similarity NPC296936
0.6559 Remote Similarity NPC121453
0.6559 Remote Similarity NPC252056
0.6559 Remote Similarity NPC90583
0.6552 Remote Similarity NPC273290
0.6552 Remote Similarity NPC232044
0.6552 Remote Similarity NPC235402
0.6543 Remote Similarity NPC472952

  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 NPC5209 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
1.0 High Similarity NPD2686 Approved
1.0 High Similarity NPD2687 Approved
1.0 High Similarity NPD2254 Approved
0.9275 High Similarity NPD1811 Approved
0.9275 High Similarity NPD1810 Approved
0.8442 Intermediate Similarity NPD3670 Clinical (unspecified phase)
0.8442 Intermediate Similarity NPD3669 Approved
0.8421 Intermediate Similarity NPD1780 Approved
0.8421 Intermediate Similarity NPD1779 Approved
0.6771 Remote Similarity NPD3710 Phase 2
0.6593 Remote Similarity NPD8171 Discontinued
0.6533 Remote Similarity NPD371 Approved
0.6353 Remote Similarity NPD6928 Phase 2
0.625 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6197 Remote Similarity NPD7346 Approved
0.5941 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5921 Remote Similarity NPD1145 Discontinued
0.5909 Remote Similarity NPD367 Approved
0.5732 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5648 Remote Similarity NPD8133 Approved
0.5616 Remote Similarity NPD893 Approved
0.5616 Remote Similarity NPD888 Phase 3
0.5616 Remote Similarity NPD891 Phase 3
0.5616 Remote Similarity NPD892 Phase 3
0.5616 Remote Similarity NPD890 Clinical (unspecified phase)
0.5612 Remote Similarity NPD7991 Discontinued

  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