Structure

Physi-Chem Properties

Molecular Weight:  220.18
Volume:  248.481
LogP:  3.926
LogD:  3.961
LogS:  -3.758
# Rotatable Bonds:  0
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.608
Synthetic Accessibility Score:  5.217
Fsp3:  0.933
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.694
MDCK Permeability:  2.2249514586292207e-05
Pgp-inhibitor:  0.672
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.831
30% Bioavailability (F30%):  0.942

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.949
Plasma Protein Binding (PPB):  54.40428924560547%
Volume Distribution (VD):  1.489
Pgp-substrate:  38.525108337402344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.227
CYP1A2-substrate:  0.412
CYP2C19-inhibitor:  0.221
CYP2C19-substrate:  0.892
CYP2C9-inhibitor:  0.155
CYP2C9-substrate:  0.156
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.569
CYP3A4-inhibitor:  0.082
CYP3A4-substrate:  0.307

ADMET: Excretion

Clearance (CL):  18.739
Half-life (T1/2):  0.127

ADMET: Toxicity

hERG Blockers:  0.074
Human Hepatotoxicity (H-HT):  0.395
Drug-inuced Liver Injury (DILI):  0.287
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.934
Maximum Recommended Daily Dose:  0.095
Skin Sensitization:  0.338
Carcinogencity:  0.856
Eye Corrosion:  0.949
Eye Irritation:  0.313
Respiratory Toxicity:  0.975

Download Data

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

  Natural Product: NPC274182

Natural Product ID:  NPC274182
Common Name*:   Suberosanone
IUPAC Name:   n.a.
Synonyms:   Suberosanone
Standard InCHIKey:  KHINYKJYBNWSSP-IAGXKZSMSA-N
Standard InCHI:  InChI=1S/C15H24O/c1-9-5-6-11-12-7-13(16)10(2)15(9,12)8-14(11,3)4/h9-12H,5-8H2,1-4H3/t9-,10-,11-,12-,15+/m0/s1
SMILES:  C[C@H]1CC[C@H]2[C@@H]3CC(=O)[C@H](C)[C@@]13CC2(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL513220
PubChem CID:   10353423
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO19653 Isis hippuris Species Isididae Eukaryota n.a. n.a. n.a. PMID[11141096]
NPO19653 Isis hippuris Species Isididae Eukaryota n.a. n.a. n.a. PMID[15974612]
NPO19653 Isis hippuris Species Isididae 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
NPT168 Cell Line P388 Mus musculus ED50 < 5.0 10'-6 ug/ml PMID[488994]
NPT81 Cell Line A549 Homo sapiens ED50 = 3.6 10'-2 ug/ml PMID[488994]
NPT139 Cell Line HT-29 Homo sapiens ED50 < 5.0 10'-6 ug/ml PMID[488994]

☑ 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 NPC274182 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
0.9574 High Similarity NPC258672
0.9574 High Similarity NPC293343
0.9574 High Similarity NPC247786
0.9362 High Similarity NPC294440
0.9149 High Similarity NPC40249
0.9149 High Similarity NPC131981
0.9149 High Similarity NPC173996
0.8571 High Similarity NPC20017
0.8491 Intermediate Similarity NPC184819
0.8393 Intermediate Similarity NPC270042
0.8367 Intermediate Similarity NPC83187
0.8367 Intermediate Similarity NPC285814
0.8367 Intermediate Similarity NPC98246
0.8333 Intermediate Similarity NPC151464
0.8333 Intermediate Similarity NPC143597
0.8333 Intermediate Similarity NPC474105
0.8302 Intermediate Similarity NPC53245
0.8302 Intermediate Similarity NPC288296
0.7872 Intermediate Similarity NPC135077
0.7872 Intermediate Similarity NPC215118
0.7872 Intermediate Similarity NPC59570
0.7872 Intermediate Similarity NPC45270
0.7797 Intermediate Similarity NPC472306
0.7755 Intermediate Similarity NPC171783
0.7447 Intermediate Similarity NPC223315
0.7377 Intermediate Similarity NPC128608
0.72 Intermediate Similarity NPC18397
0.7193 Intermediate Similarity NPC200258
0.7193 Intermediate Similarity NPC307063
0.7143 Intermediate Similarity NPC39462
0.7143 Intermediate Similarity NPC43300
0.7143 Intermediate Similarity NPC168824
0.7143 Intermediate Similarity NPC107704
0.7143 Intermediate Similarity NPC189917
0.7143 Intermediate Similarity NPC96812
0.7091 Intermediate Similarity NPC236623
0.7015 Intermediate Similarity NPC52667
0.7015 Intermediate Similarity NPC248567
0.6939 Remote Similarity NPC141634
0.6923 Remote Similarity NPC473225
0.6923 Remote Similarity NPC20610
0.6875 Remote Similarity NPC323005
0.6866 Remote Similarity NPC197701
0.6833 Remote Similarity NPC127798
0.6818 Remote Similarity NPC182815
0.6818 Remote Similarity NPC477857
0.6818 Remote Similarity NPC474962
0.6812 Remote Similarity NPC132064
0.6774 Remote Similarity NPC213152
0.6724 Remote Similarity NPC32222
0.6724 Remote Similarity NPC202146
0.6716 Remote Similarity NPC40574
0.6716 Remote Similarity NPC108131
0.6716 Remote Similarity NPC282593
0.6716 Remote Similarity NPC477856
0.6716 Remote Similarity NPC35734
0.6716 Remote Similarity NPC307176
0.6716 Remote Similarity NPC159577
0.6716 Remote Similarity NPC214770
0.6667 Remote Similarity NPC49575
0.6667 Remote Similarity NPC55004
0.6667 Remote Similarity NPC267626
0.6667 Remote Similarity NPC165695
0.662 Remote Similarity NPC169389
0.662 Remote Similarity NPC475932
0.662 Remote Similarity NPC74685
0.6618 Remote Similarity NPC58057
0.6618 Remote Similarity NPC473267
0.6618 Remote Similarity NPC470078
0.6618 Remote Similarity NPC320549
0.6618 Remote Similarity NPC305501
0.6618 Remote Similarity NPC223187
0.6618 Remote Similarity NPC115023
0.6618 Remote Similarity NPC110615
0.6618 Remote Similarity NPC151018
0.6618 Remote Similarity NPC234707
0.6618 Remote Similarity NPC156277
0.6615 Remote Similarity NPC268736
0.6615 Remote Similarity NPC477931
0.6615 Remote Similarity NPC42060
0.6613 Remote Similarity NPC84218
0.6571 Remote Similarity NPC155441
0.6567 Remote Similarity NPC131892
0.6567 Remote Similarity NPC196197
0.6567 Remote Similarity NPC327728
0.6567 Remote Similarity NPC321732
0.6567 Remote Similarity NPC213178
0.6567 Remote Similarity NPC139397
0.6567 Remote Similarity NPC324607
0.6567 Remote Similarity NPC6120
0.6562 Remote Similarity NPC212210
0.6528 Remote Similarity NPC228911
0.6522 Remote Similarity NPC310766
0.6522 Remote Similarity NPC470045
0.6522 Remote Similarity NPC303613
0.6522 Remote Similarity NPC251705
0.6522 Remote Similarity NPC232112
0.6522 Remote Similarity NPC474123
0.6522 Remote Similarity NPC474228
0.6522 Remote Similarity NPC470044
0.6515 Remote Similarity NPC130459
0.6515 Remote Similarity NPC478180
0.6515 Remote Similarity NPC474221
0.6508 Remote Similarity NPC60565
0.6471 Remote Similarity NPC265782
0.6471 Remote Similarity NPC251929
0.6471 Remote Similarity NPC476731
0.6471 Remote Similarity NPC2634
0.6471 Remote Similarity NPC260040
0.6429 Remote Similarity NPC254340
0.6429 Remote Similarity NPC255021
0.6429 Remote Similarity NPC159497
0.6429 Remote Similarity NPC472854
0.6393 Remote Similarity NPC230823
0.6393 Remote Similarity NPC192427
0.6393 Remote Similarity NPC115385
0.6377 Remote Similarity NPC54123
0.6377 Remote Similarity NPC5701
0.6377 Remote Similarity NPC89310
0.6377 Remote Similarity NPC472309
0.6377 Remote Similarity NPC126642
0.6364 Remote Similarity NPC176171
0.6349 Remote Similarity NPC127582
0.6349 Remote Similarity NPC25853
0.6349 Remote Similarity NPC478126
0.6338 Remote Similarity NPC195155
0.6338 Remote Similarity NPC255650
0.6338 Remote Similarity NPC472311
0.6338 Remote Similarity NPC125767
0.6338 Remote Similarity NPC273366
0.6338 Remote Similarity NPC97534
0.6338 Remote Similarity NPC21220
0.6338 Remote Similarity NPC174964
0.6338 Remote Similarity NPC293803
0.6338 Remote Similarity NPC72444
0.6324 Remote Similarity NPC476734
0.6324 Remote Similarity NPC64466
0.6324 Remote Similarity NPC469941
0.6324 Remote Similarity NPC319671
0.6324 Remote Similarity NPC252032
0.6316 Remote Similarity NPC116906
0.6308 Remote Similarity NPC475124
0.6308 Remote Similarity NPC285371
0.6308 Remote Similarity NPC469662
0.629 Remote Similarity NPC27610
0.629 Remote Similarity NPC56905
0.629 Remote Similarity NPC94991
0.629 Remote Similarity NPC266295
0.629 Remote Similarity NPC30215
0.6269 Remote Similarity NPC475523
0.625 Remote Similarity NPC475742
0.625 Remote Similarity NPC69408
0.625 Remote Similarity NPC5767
0.625 Remote Similarity NPC472487
0.625 Remote Similarity NPC472486
0.625 Remote Similarity NPC306750
0.6232 Remote Similarity NPC477929
0.6232 Remote Similarity NPC477850
0.6216 Remote Similarity NPC31302
0.6216 Remote Similarity NPC245029
0.6212 Remote Similarity NPC469791
0.6197 Remote Similarity NPC474796
0.6197 Remote Similarity NPC133922
0.6197 Remote Similarity NPC167702
0.6197 Remote Similarity NPC329866
0.6197 Remote Similarity NPC309852
0.6197 Remote Similarity NPC280026
0.6197 Remote Similarity NPC474797
0.619 Remote Similarity NPC472304
0.619 Remote Similarity NPC259261
0.619 Remote Similarity NPC276764
0.6167 Remote Similarity NPC319589
0.6164 Remote Similarity NPC470557
0.6164 Remote Similarity NPC471151
0.6164 Remote Similarity NPC264602
0.6164 Remote Similarity NPC91665
0.6164 Remote Similarity NPC477918
0.6164 Remote Similarity NPC475031
0.6164 Remote Similarity NPC23884
0.6164 Remote Similarity NPC221420
0.6154 Remote Similarity NPC197238
0.6154 Remote Similarity NPC202118
0.6143 Remote Similarity NPC469940
0.6143 Remote Similarity NPC311102
0.6133 Remote Similarity NPC1882
0.6119 Remote Similarity NPC84562
0.6119 Remote Similarity NPC103734
0.6111 Remote Similarity NPC469803
0.6111 Remote Similarity NPC159789
0.6111 Remote Similarity NPC212733
0.6111 Remote Similarity NPC24014
0.6111 Remote Similarity NPC27349
0.6087 Remote Similarity NPC475952
0.6081 Remote Similarity NPC82635
0.6081 Remote Similarity NPC470052
0.6081 Remote Similarity NPC469996
0.6081 Remote Similarity NPC185465
0.6081 Remote Similarity NPC63020
0.6081 Remote Similarity NPC478128
0.6061 Remote Similarity NPC6697

  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 NPC274182 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
0.9149 High Similarity NPD345 Approved
0.9149 High Similarity NPD344 Approved
0.9149 High Similarity NPD343 Approved
0.7258 Intermediate Similarity NPD3171 Clinical (unspecified phase)
0.6923 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6923 Remote Similarity NPD5360 Phase 3
0.6875 Remote Similarity NPD4224 Phase 2
0.6716 Remote Similarity NPD4747 Approved
0.6716 Remote Similarity NPD4789 Approved
0.6667 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6618 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6618 Remote Similarity NPD4758 Discontinued
0.6618 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6618 Remote Similarity NPD6081 Approved
0.6567 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6567 Remote Similarity NPD4137 Phase 3
0.6567 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6567 Remote Similarity NPD3698 Phase 2
0.6471 Remote Similarity NPD4691 Approved
0.6471 Remote Similarity NPD4245 Approved
0.6471 Remote Similarity NPD4244 Approved
0.6429 Remote Similarity NPD4687 Approved
0.6429 Remote Similarity NPD5733 Approved
0.6377 Remote Similarity NPD5276 Approved
0.6377 Remote Similarity NPD5777 Approved
0.6197 Remote Similarity NPD4058 Approved
0.6197 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6111 Remote Similarity NPD3703 Phase 2
0.6111 Remote Similarity NPD3702 Approved
0.6081 Remote Similarity NPD5364 Discontinued
0.6027 Remote Similarity NPD6117 Approved
0.5946 Remote Similarity NPD6116 Phase 1
0.5902 Remote Similarity NPD615 Clinical (unspecified phase)
0.5867 Remote Similarity NPD4776 Phase 2
0.5867 Remote Similarity NPD6115 Approved
0.5867 Remote Similarity NPD6697 Approved
0.5867 Remote Similarity NPD6114 Approved
0.5867 Remote Similarity NPD4777 Suspended
0.5867 Remote Similarity NPD3617 Approved
0.5867 Remote Similarity NPD3671 Phase 1
0.5867 Remote Similarity NPD6118 Approved
0.5844 Remote Similarity NPD4692 Approved
0.5844 Remote Similarity NPD4139 Approved
0.5781 Remote Similarity NPD287 Approved
0.5769 Remote Similarity NPD4221 Approved
0.5769 Remote Similarity NPD4223 Phase 3
0.5696 Remote Similarity NPD4788 Approved
0.5636 Remote Similarity NPD387 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4197 Approved
0.5625 Remote Similarity NPD4786 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