Structure

Physi-Chem Properties

Molecular Weight:  236.18
Volume:  257.271
LogP:  3.026
LogD:  3.883
LogS:  -3.593
# Rotatable Bonds:  2
TPSA:  29.46
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.448
Synthetic Accessibility Score:  4.9
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.533
MDCK Permeability:  2.201294046244584e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.035
30% Bioavailability (F30%):  0.011

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.72
Plasma Protein Binding (PPB):  77.94612121582031%
Volume Distribution (VD):  1.298
Pgp-substrate:  17.183637619018555%

ADMET: Metabolism

CYP1A2-inhibitor:  0.426
CYP1A2-substrate:  0.893
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.893
CYP2C9-inhibitor:  0.033
CYP2C9-substrate:  0.464
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.795
CYP3A4-inhibitor:  0.18
CYP3A4-substrate:  0.271

ADMET: Excretion

Clearance (CL):  8.039
Half-life (T1/2):  0.575

ADMET: Toxicity

hERG Blockers:  0.092
Human Hepatotoxicity (H-HT):  0.476
Drug-inuced Liver Injury (DILI):  0.481
AMES Toxicity:  0.649
Rat Oral Acute Toxicity:  0.127
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.516
Carcinogencity:  0.696
Eye Corrosion:  0.963
Eye Irritation:  0.969
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC162109

Natural Product ID:  NPC162109
Common Name*:   YQCPSQZKRUVQOR-DXUDUQDWSA-N
IUPAC Name:   n.a.
Synonyms:   8Beta-Hydroperoxyprespatane
Standard InCHIKey:  YQCPSQZKRUVQOR-DXUDUQDWSA-N
Standard InCHI:  InChI=1S/C15H24O2/c1-9(2)15(17-16)8-7-14(4)11-6-5-10(3)12(11)13(14)15/h10-13,16H,1,5-8H2,2-4H3/t10-,11+,12-,13+,14-,15+/m1/s1
SMILES:  OO[C@@]1(CC[C@]2([C@@H]1[C@@H]1[C@H](C)CC[C@H]21)C)C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL251692
PubChem CID:   23642713
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. formosan soft coral n.a. PMID[17845002]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[24370010]
NPO13916 Nephthea erecta Species Nephtheidae Eukaryota n.a. n.a. n.a. PMID[9722490]
NPO13916 Nephthea erecta Species Nephtheidae 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
NPT139 Cell Line HT-29 Homo sapiens ED50 = 0.5 ug ml-1 PMID[485304]
NPT168 Cell Line P388 Mus musculus ED50 = 0.3 ug ml-1 PMID[485304]

☑ 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 NPC162109 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
0.9153 High Similarity NPC15152
0.7903 Intermediate Similarity NPC99480
0.7903 Intermediate Similarity NPC184049
0.7794 Intermediate Similarity NPC133873
0.7746 Intermediate Similarity NPC310643
0.7619 Intermediate Similarity NPC52431
0.7619 Intermediate Similarity NPC310228
0.7538 Intermediate Similarity NPC474480
0.75 Intermediate Similarity NPC472472
0.75 Intermediate Similarity NPC252809
0.7465 Intermediate Similarity NPC309178
0.7385 Intermediate Similarity NPC63111
0.7353 Intermediate Similarity NPC308522
0.7353 Intermediate Similarity NPC74885
0.7344 Intermediate Similarity NPC5698
0.7324 Intermediate Similarity NPC14352
0.7324 Intermediate Similarity NPC234527
0.7237 Intermediate Similarity NPC472471
0.7231 Intermediate Similarity NPC323153
0.7183 Intermediate Similarity NPC471660
0.7164 Intermediate Similarity NPC219940
0.7143 Intermediate Similarity NPC51762
0.7143 Intermediate Similarity NPC472465
0.7143 Intermediate Similarity NPC474118
0.7123 Intermediate Similarity NPC313185
0.7121 Intermediate Similarity NPC147524
0.7101 Intermediate Similarity NPC136813
0.7101 Intermediate Similarity NPC477791
0.7077 Intermediate Similarity NPC469321
0.7059 Intermediate Similarity NPC261782
0.7059 Intermediate Similarity NPC205618
0.7059 Intermediate Similarity NPC469326
0.7059 Intermediate Similarity NPC238352
0.7059 Intermediate Similarity NPC477009
0.7042 Intermediate Similarity NPC254845
0.7031 Intermediate Similarity NPC278550
0.6986 Remote Similarity NPC471659
0.697 Remote Similarity NPC135648
0.6957 Remote Similarity NPC162309
0.6957 Remote Similarity NPC469328
0.6892 Remote Similarity NPC201263
0.6883 Remote Similarity NPC80622
0.6883 Remote Similarity NPC472470
0.6866 Remote Similarity NPC210346
0.6835 Remote Similarity NPC472473
0.6825 Remote Similarity NPC286752
0.6812 Remote Similarity NPC300442
0.68 Remote Similarity NPC126969
0.68 Remote Similarity NPC471658
0.6786 Remote Similarity NPC473614
0.6769 Remote Similarity NPC65786
0.6769 Remote Similarity NPC7491
0.6769 Remote Similarity NPC101285
0.6769 Remote Similarity NPC13789
0.6769 Remote Similarity NPC27853
0.6761 Remote Similarity NPC167527
0.6761 Remote Similarity NPC224532
0.6757 Remote Similarity NPC474524
0.6757 Remote Similarity NPC475517
0.6712 Remote Similarity NPC41886
0.6667 Remote Similarity NPC309300
0.6667 Remote Similarity NPC144647
0.6667 Remote Similarity NPC140233
0.6667 Remote Similarity NPC287744
0.6667 Remote Similarity NPC22301
0.6625 Remote Similarity NPC260852
0.6623 Remote Similarity NPC477514
0.6622 Remote Similarity NPC472506
0.6615 Remote Similarity NPC39068
0.6615 Remote Similarity NPC264779
0.6613 Remote Similarity NPC251335
0.6575 Remote Similarity NPC471781
0.6552 Remote Similarity NPC141777
0.6552 Remote Similarity NPC227670
0.6552 Remote Similarity NPC166362
0.6538 Remote Similarity NPC49599
0.6538 Remote Similarity NPC49627
0.6533 Remote Similarity NPC476736
0.6486 Remote Similarity NPC471662
0.6486 Remote Similarity NPC164045
0.6471 Remote Similarity NPC40206
0.6471 Remote Similarity NPC472466
0.6462 Remote Similarity NPC89069
0.6462 Remote Similarity NPC166894
0.6462 Remote Similarity NPC45387
0.6462 Remote Similarity NPC283655
0.6462 Remote Similarity NPC277917
0.6462 Remote Similarity NPC178223
0.6447 Remote Similarity NPC23231
0.6447 Remote Similarity NPC251435
0.6447 Remote Similarity NPC85831
0.6447 Remote Similarity NPC265921
0.6447 Remote Similarity NPC60818
0.6447 Remote Similarity NPC215215
0.6447 Remote Similarity NPC77501
0.6438 Remote Similarity NPC474900
0.642 Remote Similarity NPC471340
0.6418 Remote Similarity NPC474769
0.6418 Remote Similarity NPC189290
0.641 Remote Similarity NPC472501
0.641 Remote Similarity NPC42853
0.6406 Remote Similarity NPC192962
0.64 Remote Similarity NPC310608
0.6395 Remote Similarity NPC472468
0.6389 Remote Similarity NPC161612
0.6389 Remote Similarity NPC33583
0.6377 Remote Similarity NPC41160
0.6375 Remote Similarity NPC471661
0.6364 Remote Similarity NPC38141
0.6364 Remote Similarity NPC476317
0.6364 Remote Similarity NPC152017
0.6351 Remote Similarity NPC18543
0.6351 Remote Similarity NPC475728
0.6341 Remote Similarity NPC242016
0.6338 Remote Similarity NPC19569
0.6338 Remote Similarity NPC258595
0.6333 Remote Similarity NPC229403
0.6316 Remote Similarity NPC206875
0.6316 Remote Similarity NPC329090
0.6316 Remote Similarity NPC27395
0.6308 Remote Similarity NPC202146
0.6308 Remote Similarity NPC32222
0.6296 Remote Similarity NPC20262
0.6296 Remote Similarity NPC256750
0.629 Remote Similarity NPC95969
0.629 Remote Similarity NPC127997
0.6286 Remote Similarity NPC50435
0.6286 Remote Similarity NPC211291
0.6286 Remote Similarity NPC474155
0.6286 Remote Similarity NPC133368
0.6286 Remote Similarity NPC124112
0.6286 Remote Similarity NPC473759
0.6282 Remote Similarity NPC138502
0.6282 Remote Similarity NPC260301
0.6282 Remote Similarity NPC475025
0.6282 Remote Similarity NPC475027
0.6282 Remote Similarity NPC186109
0.6282 Remote Similarity NPC307336
0.6282 Remote Similarity NPC474230
0.6269 Remote Similarity NPC291147
0.6269 Remote Similarity NPC29976
0.6269 Remote Similarity NPC150713
0.6267 Remote Similarity NPC469737
0.6265 Remote Similarity NPC318390
0.625 Remote Similarity NPC230107
0.625 Remote Similarity NPC471656
0.625 Remote Similarity NPC40417
0.625 Remote Similarity NPC475897
0.625 Remote Similarity NPC476406
0.625 Remote Similarity NPC294358
0.625 Remote Similarity NPC472467
0.6234 Remote Similarity NPC3403
0.6234 Remote Similarity NPC328104
0.6234 Remote Similarity NPC113639
0.6234 Remote Similarity NPC185536
0.6234 Remote Similarity NPC319090
0.6232 Remote Similarity NPC47840
0.6232 Remote Similarity NPC234264
0.6232 Remote Similarity NPC84218
0.622 Remote Similarity NPC474748
0.6216 Remote Similarity NPC217570
0.6216 Remote Similarity NPC90115
0.6216 Remote Similarity NPC469677
0.6203 Remote Similarity NPC472342
0.6203 Remote Similarity NPC470944
0.6203 Remote Similarity NPC477819
0.6203 Remote Similarity NPC477522
0.6203 Remote Similarity NPC475
0.6203 Remote Similarity NPC472499
0.6203 Remote Similarity NPC301707
0.6203 Remote Similarity NPC477817
0.6203 Remote Similarity NPC473943
0.6203 Remote Similarity NPC472500
0.6203 Remote Similarity NPC472502
0.6197 Remote Similarity NPC101128
0.619 Remote Similarity NPC131623
0.6184 Remote Similarity NPC469320
0.6184 Remote Similarity NPC300940
0.6184 Remote Similarity NPC329763
0.6184 Remote Similarity NPC92909
0.6184 Remote Similarity NPC107783
0.6184 Remote Similarity NPC474140
0.6173 Remote Similarity NPC47761
0.6164 Remote Similarity NPC472253
0.6164 Remote Similarity NPC472255
0.6154 Remote Similarity NPC315261
0.6154 Remote Similarity NPC91573
0.6154 Remote Similarity NPC474231
0.6154 Remote Similarity NPC96319
0.6154 Remote Similarity NPC215481
0.6145 Remote Similarity NPC116613
0.6129 Remote Similarity NPC100445
0.6125 Remote Similarity NPC5604
0.6125 Remote Similarity NPC24504
0.6125 Remote Similarity NPC301769
0.6125 Remote Similarity NPC32758
0.6125 Remote Similarity NPC476316
0.6125 Remote Similarity NPC1319
0.6119 Remote Similarity NPC24443
0.6119 Remote Similarity NPC274396

  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 NPC162109 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
0.6712 Remote Similarity NPD4243 Approved
0.6533 Remote Similarity NPD4784 Approved
0.6533 Remote Similarity NPD4785 Approved
0.6447 Remote Similarity NPD5275 Approved
0.6447 Remote Similarity NPD4190 Phase 3
0.6329 Remote Similarity NPD4195 Approved
0.6316 Remote Similarity NPD6926 Approved
0.6316 Remote Similarity NPD6924 Approved
0.6154 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6933 Approved
0.6098 Remote Similarity NPD4221 Approved
0.6098 Remote Similarity NPD4223 Phase 3
0.6049 Remote Similarity NPD6930 Phase 2
0.6049 Remote Similarity NPD6931 Approved
0.6024 Remote Similarity NPD4788 Approved
0.5952 Remote Similarity NPD4197 Approved
0.593 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5926 Remote Similarity NPD6929 Approved
0.5882 Remote Similarity NPD5329 Approved
0.5854 Remote Similarity NPD7525 Registered
0.5854 Remote Similarity NPD4748 Discontinued
0.5833 Remote Similarity NPD5332 Approved
0.5833 Remote Similarity NPD6695 Phase 3
0.5833 Remote Similarity NPD5331 Approved
0.5823 Remote Similarity NPD6942 Approved
0.5823 Remote Similarity NPD7339 Approved
0.5814 Remote Similarity NPD4693 Phase 3
0.5814 Remote Similarity NPD4689 Approved
0.5814 Remote Similarity NPD5690 Phase 2
0.5814 Remote Similarity NPD5205 Approved
0.5814 Remote Similarity NPD4688 Approved
0.5814 Remote Similarity NPD5280 Approved
0.5814 Remote Similarity NPD4690 Approved
0.5814 Remote Similarity NPD4138 Approved
0.5814 Remote Similarity NPD4694 Approved
0.5789 Remote Similarity NPD6923 Approved
0.5789 Remote Similarity NPD6922 Approved
0.5783 Remote Similarity NPD4139 Approved
0.5783 Remote Similarity NPD4790 Discontinued
0.5783 Remote Similarity NPD4692 Approved
0.5775 Remote Similarity NPD1145 Discontinued
0.5765 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5714 Remote Similarity NPD7144 Approved
0.5714 Remote Similarity NPD7143 Approved
0.5698 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5698 Remote Similarity NPD6893 Approved
0.5682 Remote Similarity NPD4518 Approved
0.5682 Remote Similarity NPD4723 Approved
0.5682 Remote Similarity NPD4722 Approved
0.5679 Remote Similarity NPD5776 Phase 2
0.5679 Remote Similarity NPD6925 Approved
0.5679 Remote Similarity NPD6932 Approved
0.5663 Remote Similarity NPD7509 Discontinued
0.5663 Remote Similarity NPD7514 Phase 3
0.5647 Remote Similarity NPD5362 Discontinued
0.5641 Remote Similarity NPD7151 Approved
0.5641 Remote Similarity NPD7152 Approved
0.5641 Remote Similarity NPD7150 Approved
0.5632 Remote Similarity NPD6098 Approved
0.5618 Remote Similarity NPD6051 Approved
0.5618 Remote Similarity NPD4753 Phase 2
0.561 Remote Similarity NPD7322 Clinical (unspecified phase)
0.561 Remote Similarity NPD7145 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