Structure

Physi-Chem Properties

Molecular Weight:  270.18
Volume:  277.488
LogP:  2.159
LogD:  1.819
LogS:  -2.631
# Rotatable Bonds:  1
TPSA:  65.52
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.708
Synthetic Accessibility Score:  5.155
Fsp3:  1.0
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:  -4.549
MDCK Permeability:  1.4043681403563824e-05
Pgp-inhibitor:  0.685
Pgp-substrate:  0.219
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.04

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.23
Plasma Protein Binding (PPB):  68.9471664428711%
Volume Distribution (VD):  1.295
Pgp-substrate:  30.59037971496582%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.814
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.862
CYP2C9-inhibitor:  0.019
CYP2C9-substrate:  0.038
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.081
CYP3A4-substrate:  0.325

ADMET: Excretion

Clearance (CL):  10.615
Half-life (T1/2):  0.36

ADMET: Toxicity

hERG Blockers:  0.061
Human Hepatotoxicity (H-HT):  0.222
Drug-inuced Liver Injury (DILI):  0.047
AMES Toxicity:  0.162
Rat Oral Acute Toxicity:  0.441
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.624
Carcinogencity:  0.318
Eye Corrosion:  0.88
Eye Irritation:  0.447
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: NPC172622

Natural Product ID:  NPC172622
Common Name*:   DGXAQSCCBAJJAS-OXWFSDFCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DGXAQSCCBAJJAS-OXWFSDFCSA-N
Standard InCHI:  InChI=1S/C15H26O4/c1-8(2)9-5-6-14(3)12(18-14)10(16)7-15(4)13(19-15)11(9)17/h8-13,16-17H,5-7H2,1-4H3/t9-,10+,11+,12-,13-,14-,15-/m0/s1
SMILES:  CC(C)[C@@H]1CC[C@@]2(C)[C@H]([C@@H](C[C@@]3(C)[C@H]([C@@H]1O)O3)O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL501300
PubChem CID:   15699881
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane sesquiterpenoids

*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
NPO29822 Santolina insularis Species Asteraceae Eukaryota aerial parts n.a. n.a. PMID[15974607]
NPO29822 Santolina insularis Species Asteraceae Eukaryota n.a. aerial part n.a. PMID[15974607]

☑ 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
NPT27 Others Unspecified IC50 >= 10.0 ug.mL-1 PMID[496527]

☑ 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 NPC172622 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
0.8413 Intermediate Similarity NPC476702
0.7917 Intermediate Similarity NPC470014
0.7846 Intermediate Similarity NPC199937
0.7627 Intermediate Similarity NPC474331
0.7538 Intermediate Similarity NPC475807
0.746 Intermediate Similarity NPC322148
0.7385 Intermediate Similarity NPC475412
0.7302 Intermediate Similarity NPC170780
0.726 Intermediate Similarity NPC472952
0.726 Intermediate Similarity NPC472950
0.7206 Intermediate Similarity NPC165069
0.7162 Intermediate Similarity NPC170148
0.7123 Intermediate Similarity NPC190859
0.7077 Intermediate Similarity NPC476209
0.7077 Intermediate Similarity NPC182903
0.7 Intermediate Similarity NPC179823
0.6986 Remote Similarity NPC143576
0.6986 Remote Similarity NPC476709
0.697 Remote Similarity NPC185116
0.6957 Remote Similarity NPC250836
0.6923 Remote Similarity NPC119425
0.6892 Remote Similarity NPC470151
0.6892 Remote Similarity NPC166250
0.6842 Remote Similarity NPC188793
0.6842 Remote Similarity NPC476703
0.6842 Remote Similarity NPC108014
0.6795 Remote Similarity NPC186588
0.6795 Remote Similarity NPC472951
0.6795 Remote Similarity NPC472943
0.6761 Remote Similarity NPC33583
0.6761 Remote Similarity NPC477759
0.6761 Remote Similarity NPC477760
0.6761 Remote Similarity NPC477754
0.6761 Remote Similarity NPC161612
0.6761 Remote Similarity NPC477758
0.6761 Remote Similarity NPC477761
0.6757 Remote Similarity NPC470660
0.6757 Remote Similarity NPC470659
0.6753 Remote Similarity NPC477089
0.675 Remote Similarity NPC231601
0.6721 Remote Similarity NPC224987
0.6711 Remote Similarity NPC293223
0.6711 Remote Similarity NPC136424
0.6711 Remote Similarity NPC279575
0.6709 Remote Similarity NPC473257
0.6667 Remote Similarity NPC308489
0.6667 Remote Similarity NPC138273
0.6667 Remote Similarity NPC50435
0.6622 Remote Similarity NPC470173
0.662 Remote Similarity NPC477752
0.662 Remote Similarity NPC477756
0.662 Remote Similarity NPC477751
0.662 Remote Similarity NPC477764
0.6582 Remote Similarity NPC186594
0.6582 Remote Similarity NPC66766
0.6582 Remote Similarity NPC117137
0.6582 Remote Similarity NPC16449
0.6579 Remote Similarity NPC36479
0.6575 Remote Similarity NPC253123
0.6571 Remote Similarity NPC94897
0.6562 Remote Similarity NPC161473
0.6538 Remote Similarity NPC272841
0.6538 Remote Similarity NPC43463
0.6538 Remote Similarity NPC191345
0.6538 Remote Similarity NPC177343
0.6538 Remote Similarity NPC252483
0.6538 Remote Similarity NPC52755
0.6533 Remote Similarity NPC248427
0.6528 Remote Similarity NPC286842
0.6512 Remote Similarity NPC475881
0.6512 Remote Similarity NPC70251
0.65 Remote Similarity NPC216941
0.6494 Remote Similarity NPC268111
0.6486 Remote Similarity NPC471879
0.6471 Remote Similarity NPC475968
0.6456 Remote Similarity NPC170595
0.6447 Remote Similarity NPC471525
0.6447 Remote Similarity NPC470630
0.642 Remote Similarity NPC216800
0.642 Remote Similarity NPC212340
0.642 Remote Similarity NPC475849
0.641 Remote Similarity NPC214030
0.641 Remote Similarity NPC476719
0.641 Remote Similarity NPC83108
0.6393 Remote Similarity NPC8597
0.6364 Remote Similarity NPC93213
0.6351 Remote Similarity NPC470833
0.6341 Remote Similarity NPC474266
0.6341 Remote Similarity NPC227170
0.6341 Remote Similarity NPC260852
0.6329 Remote Similarity NPC471769
0.6324 Remote Similarity NPC47663
0.6322 Remote Similarity NPC474699
0.631 Remote Similarity NPC475729
0.631 Remote Similarity NPC474215
0.6296 Remote Similarity NPC470156
0.6296 Remote Similarity NPC118116
0.6296 Remote Similarity NPC211049
0.6282 Remote Similarity NPC470176
0.6282 Remote Similarity NPC329626
0.6269 Remote Similarity NPC24443
0.6269 Remote Similarity NPC148424
0.6265 Remote Similarity NPC474156
0.625 Remote Similarity NPC477282
0.625 Remote Similarity NPC81074
0.625 Remote Similarity NPC476701
0.625 Remote Similarity NPC307022
0.625 Remote Similarity NPC472946
0.625 Remote Similarity NPC471200
0.6234 Remote Similarity NPC53868
0.6234 Remote Similarity NPC472945
0.6234 Remote Similarity NPC472944
0.6234 Remote Similarity NPC200167
0.6234 Remote Similarity NPC31046
0.6234 Remote Similarity NPC209666
0.6232 Remote Similarity NPC470363
0.623 Remote Similarity NPC77550
0.623 Remote Similarity NPC108441
0.622 Remote Similarity NPC477446
0.622 Remote Similarity NPC475388
0.622 Remote Similarity NPC477447
0.622 Remote Similarity NPC470155
0.6203 Remote Similarity NPC11907
0.6203 Remote Similarity NPC133596
0.6203 Remote Similarity NPC474574
0.6203 Remote Similarity NPC64081
0.6203 Remote Similarity NPC474003
0.6203 Remote Similarity NPC476233
0.619 Remote Similarity NPC82512
0.6184 Remote Similarity NPC96322
0.6176 Remote Similarity NPC219040
0.6176 Remote Similarity NPC291147
0.6167 Remote Similarity NPC144891
0.6164 Remote Similarity NPC469328
0.6163 Remote Similarity NPC476379
0.6154 Remote Similarity NPC244869
0.6154 Remote Similarity NPC300235
0.6154 Remote Similarity NPC476136
0.6154 Remote Similarity NPC476149
0.6145 Remote Similarity NPC241959
0.6145 Remote Similarity NPC239308
0.6145 Remote Similarity NPC477978
0.6143 Remote Similarity NPC472026
0.6133 Remote Similarity NPC16964
0.6133 Remote Similarity NPC74722
0.6133 Remote Similarity NPC304690
0.6129 Remote Similarity NPC147343
0.6129 Remote Similarity NPC287550
0.6129 Remote Similarity NPC223468
0.6129 Remote Similarity NPC198540
0.6129 Remote Similarity NPC88638
0.6129 Remote Similarity NPC84030
0.6129 Remote Similarity NPC176309
0.6119 Remote Similarity NPC471269
0.6118 Remote Similarity NPC228593
0.6118 Remote Similarity NPC235196
0.6118 Remote Similarity NPC472745
0.6118 Remote Similarity NPC64862
0.6098 Remote Similarity NPC116320
0.6098 Remote Similarity NPC246621
0.6098 Remote Similarity NPC119922
0.6098 Remote Similarity NPC470154
0.6087 Remote Similarity NPC474213
0.6081 Remote Similarity NPC163290
0.6081 Remote Similarity NPC469925
0.6081 Remote Similarity NPC259299
0.6076 Remote Similarity NPC107963
0.6076 Remote Similarity NPC470174
0.6076 Remote Similarity NPC470145
0.6071 Remote Similarity NPC166279
0.6071 Remote Similarity NPC18953
0.6066 Remote Similarity NPC62014
0.6066 Remote Similarity NPC240994
0.6047 Remote Similarity NPC202937
0.6044 Remote Similarity NPC477264
0.6027 Remote Similarity NPC474402
0.6027 Remote Similarity NPC61503
0.6026 Remote Similarity NPC475458
0.6 Remote Similarity NPC23134
0.6 Remote Similarity NPC471379
0.6 Remote Similarity NPC124963
0.6 Remote Similarity NPC305698
0.6 Remote Similarity NPC290612
0.6 Remote Similarity NPC298595
0.6 Remote Similarity NPC30687
0.6 Remote Similarity NPC233726
0.6 Remote Similarity NPC196911
0.6 Remote Similarity NPC244002
0.6 Remote Similarity NPC476715
0.5978 Remote Similarity NPC476040
0.5978 Remote Similarity NPC476021
0.5978 Remote Similarity NPC474994
0.5977 Remote Similarity NPC476704
0.5977 Remote Similarity NPC476707
0.5977 Remote Similarity NPC470872
0.5977 Remote Similarity NPC476706
0.5976 Remote Similarity NPC474739
0.5976 Remote Similarity NPC100697
0.5974 Remote Similarity NPC157777
0.5974 Remote Similarity NPC470071

  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 NPC172622 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
0.7313 Intermediate Similarity NPD371 Approved
0.6842 Remote Similarity NPD8958 Phase 2
0.6486 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6234 Remote Similarity NPD1811 Approved
0.6234 Remote Similarity NPD1810 Approved
0.623 Remote Similarity NPD386 Approved
0.623 Remote Similarity NPD388 Approved
0.6129 Remote Similarity NPD385 Approved
0.6129 Remote Similarity NPD384 Approved
0.6029 Remote Similarity NPD2267 Suspended
0.5843 Remote Similarity NPD3168 Discontinued
0.5806 Remote Similarity NPD9218 Clinical (unspecified phase)
0.5806 Remote Similarity NPD9219 Approved
0.5789 Remote Similarity NPD5344 Discontinued
0.5758 Remote Similarity NPD904 Phase 3
0.5758 Remote Similarity NPD905 Approved
0.5738 Remote Similarity NPD1462 Approved
0.5738 Remote Similarity NPD8957 Approved
0.5714 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5676 Remote Similarity NPD7909 Approved
0.5667 Remote Similarity NPD1460 Approved
0.5667 Remote Similarity NPD7838 Discovery
0.5667 Remote Similarity NPD7536 Approved
0.5645 Remote Similarity NPD9006 Approved
0.5641 Remote Similarity NPD2254 Approved
0.5641 Remote Similarity NPD2686 Approved
0.5641 Remote Similarity NPD2687 Approved
0.5614 Remote Similarity NPD9052 Approved
0.5614 Remote Similarity NPD9053 Approved
0.5614 Remote Similarity NPD9051 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