Structure

Physi-Chem Properties

Molecular Weight:  252.21
Volume:  277.203
LogP:  4.924
LogD:  4.082
LogS:  -4.056
# Rotatable Bonds:  1
TPSA:  18.46
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.706
Synthetic Accessibility Score:  4.174
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.579
MDCK Permeability:  1.7796446627471596e-05
Pgp-inhibitor:  0.983
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.957
30% Bioavailability (F30%):  0.686

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.274
Plasma Protein Binding (PPB):  79.61486053466797%
Volume Distribution (VD):  1.89
Pgp-substrate:  19.834026336669922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.041
CYP1A2-substrate:  0.771
CYP2C19-inhibitor:  0.079
CYP2C19-substrate:  0.867
CYP2C9-inhibitor:  0.183
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.363
CYP3A4-inhibitor:  0.117
CYP3A4-substrate:  0.267

ADMET: Excretion

Clearance (CL):  13.206
Half-life (T1/2):  0.098

ADMET: Toxicity

hERG Blockers:  0.112
Human Hepatotoxicity (H-HT):  0.162
Drug-inuced Liver Injury (DILI):  0.404
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.356
Maximum Recommended Daily Dose:  0.041
Skin Sensitization:  0.935
Carcinogencity:  0.645
Eye Corrosion:  0.978
Eye Irritation:  0.945
Respiratory Toxicity:  0.956

Download Data

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

  Natural Product: NPC132998

Natural Product ID:  NPC132998
Common Name*:   (1R,3As,5As,9As,9Bs)-1-Methoxy-6,6,9A-Trimethyldodecahydronaphtho[2,1-C]Furan
IUPAC Name:   (1R,3aS,5aS,9aS,9bS)-1-methoxy-6,6,9a-trimethyl-1,3,3a,4,5,5a,7,8,9,9b-decahydrobenzo[e][2]benzofuran
Synonyms:  
Standard InCHIKey:  SCPFXJGXNYBOFM-SGPHBRAGSA-N
Standard InCHI:  InChI=1S/C16H28O2/c1-15(2)8-5-9-16(3)12(15)7-6-11-10-18-14(17-4)13(11)16/h11-14H,5-10H2,1-4H3/t11-,12+,13-,14-,16+/m1/s1
SMILES:  CC1(C)CCC[C@@]2(C)[C@H]1CC[C@@H]1CO[C@H]([C@H]21)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463214
PubChem CID:   10729514
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001634] Naphthofurans

*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
NPO30670 Dysidea Genus Dysideidae Eukaryota n.a. n.a. n.a. PMID[11374954]
NPO30670 Dysidea Genus Dysideidae Eukaryota n.a. n.a. n.a. PMID[21214221]
NPO30670 Dysidea Genus Dysideidae Eukaryota n.a. n.a. n.a. PMID[9392880]

☑ 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
NPT773 Organism Photobacterium leiognathi Photobacterium leiognathi IC50 = 90000.0 nM PMID[523768]

☑ 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 NPC132998 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
0.7465 Intermediate Similarity NPC107963
0.7344 Intermediate Similarity NPC306750
0.7297 Intermediate Similarity NPC471217
0.7297 Intermediate Similarity NPC471216
0.7297 Intermediate Similarity NPC475456
0.7286 Intermediate Similarity NPC12680
0.72 Intermediate Similarity NPC71541
0.7027 Intermediate Similarity NPC177343
0.7013 Intermediate Similarity NPC474346
0.7013 Intermediate Similarity NPC474253
0.7013 Intermediate Similarity NPC475820
0.7013 Intermediate Similarity NPC213737
0.7013 Intermediate Similarity NPC474284
0.7 Intermediate Similarity NPC51956
0.7 Intermediate Similarity NPC5209
0.7 Intermediate Similarity NPC29005
0.6984 Remote Similarity NPC236588
0.6944 Remote Similarity NPC308489
0.6933 Remote Similarity NPC474754
0.6923 Remote Similarity NPC101138
0.6923 Remote Similarity NPC204173
0.6923 Remote Similarity NPC471367
0.6923 Remote Similarity NPC51135
0.6923 Remote Similarity NPC82492
0.6923 Remote Similarity NPC25802
0.6883 Remote Similarity NPC208912
0.6883 Remote Similarity NPC2096
0.6875 Remote Similarity NPC476735
0.6857 Remote Similarity NPC295788
0.6842 Remote Similarity NPC473685
0.6842 Remote Similarity NPC248944
0.6842 Remote Similarity NPC7479
0.6842 Remote Similarity NPC186588
0.6842 Remote Similarity NPC257296
0.6835 Remote Similarity NPC235402
0.6812 Remote Similarity NPC476928
0.6806 Remote Similarity NPC109510
0.68 Remote Similarity NPC477577
0.675 Remote Similarity NPC118266
0.675 Remote Similarity NPC471410
0.675 Remote Similarity NPC474008
0.675 Remote Similarity NPC471369
0.675 Remote Similarity NPC471411
0.675 Remote Similarity NPC173917
0.6719 Remote Similarity NPC135438
0.6711 Remote Similarity NPC17550
0.6709 Remote Similarity NPC18953
0.6667 Remote Similarity NPC122945
0.6667 Remote Similarity NPC470611
0.6667 Remote Similarity NPC24556
0.6667 Remote Similarity NPC109938
0.6667 Remote Similarity NPC84562
0.6667 Remote Similarity NPC296734
0.6625 Remote Similarity NPC290612
0.6585 Remote Similarity NPC263079
0.6585 Remote Similarity NPC33398
0.6585 Remote Similarity NPC319030
0.6585 Remote Similarity NPC221993
0.6585 Remote Similarity NPC470872
0.6582 Remote Similarity NPC470070
0.6582 Remote Similarity NPC324243
0.6582 Remote Similarity NPC241959
0.6579 Remote Similarity NPC272841
0.6575 Remote Similarity NPC253805
0.6575 Remote Similarity NPC474755
0.6543 Remote Similarity NPC244174
0.6543 Remote Similarity NPC471368
0.6543 Remote Similarity NPC268633
0.6538 Remote Similarity NPC474870
0.6538 Remote Similarity NPC271572
0.6528 Remote Similarity NPC282454
0.6528 Remote Similarity NPC471879
0.6522 Remote Similarity NPC472946
0.6506 Remote Similarity NPC20822
0.6506 Remote Similarity NPC293044
0.6506 Remote Similarity NPC473058
0.6506 Remote Similarity NPC82955
0.65 Remote Similarity NPC227260
0.65 Remote Similarity NPC474156
0.65 Remote Similarity NPC79308
0.6486 Remote Similarity NPC472944
0.6486 Remote Similarity NPC53868
0.6486 Remote Similarity NPC200167
0.6486 Remote Similarity NPC209666
0.6486 Remote Similarity NPC31046
0.6486 Remote Similarity NPC55508
0.6486 Remote Similarity NPC472945
0.6471 Remote Similarity NPC114891
0.6463 Remote Similarity NPC140446
0.6463 Remote Similarity NPC110365
0.6463 Remote Similarity NPC213658
0.6463 Remote Similarity NPC45833
0.6463 Remote Similarity NPC62202
0.6463 Remote Similarity NPC43912
0.6438 Remote Similarity NPC109457
0.6438 Remote Similarity NPC469940
0.6438 Remote Similarity NPC100586
0.6438 Remote Similarity NPC157422
0.6429 Remote Similarity NPC471370
0.6429 Remote Similarity NPC159876
0.6429 Remote Similarity NPC473542
0.6429 Remote Similarity NPC471371
0.6429 Remote Similarity NPC44122
0.642 Remote Similarity NPC273290
0.642 Remote Similarity NPC232044
0.642 Remote Similarity NPC300985
0.6418 Remote Similarity NPC84218
0.641 Remote Similarity NPC60568
0.641 Remote Similarity NPC206062
0.6406 Remote Similarity NPC300189
0.64 Remote Similarity NPC472952
0.64 Remote Similarity NPC478105
0.64 Remote Similarity NPC472950
0.6389 Remote Similarity NPC178541
0.6386 Remote Similarity NPC281004
0.6386 Remote Similarity NPC144069
0.6377 Remote Similarity NPC118937
0.6377 Remote Similarity NPC281540
0.6377 Remote Similarity NPC159654
0.6377 Remote Similarity NPC167995
0.6375 Remote Similarity NPC472440
0.6353 Remote Similarity NPC5632
0.6353 Remote Similarity NPC229801
0.6353 Remote Similarity NPC307167
0.6353 Remote Similarity NPC59006
0.6353 Remote Similarity NPC210759
0.6353 Remote Similarity NPC475878
0.6353 Remote Similarity NPC149966
0.6349 Remote Similarity NPC36002
0.6349 Remote Similarity NPC102336
0.6341 Remote Similarity NPC107603
0.6329 Remote Similarity NPC472229
0.6329 Remote Similarity NPC472230
0.6324 Remote Similarity NPC218585
0.6324 Remote Similarity NPC148174
0.6324 Remote Similarity NPC71460
0.631 Remote Similarity NPC131466
0.631 Remote Similarity NPC473472
0.631 Remote Similarity NPC470819
0.631 Remote Similarity NPC102725
0.6301 Remote Similarity NPC477929
0.6296 Remote Similarity NPC319238
0.6296 Remote Similarity NPC71626
0.6296 Remote Similarity NPC469569
0.629 Remote Similarity NPC291724
0.629 Remote Similarity NPC274261
0.6286 Remote Similarity NPC474768
0.6286 Remote Similarity NPC475943
0.6286 Remote Similarity NPC477603
0.6286 Remote Similarity NPC243469
0.6286 Remote Similarity NPC190827
0.6282 Remote Similarity NPC477287
0.6279 Remote Similarity NPC234352
0.6279 Remote Similarity NPC311246
0.6279 Remote Similarity NPC224003
0.6279 Remote Similarity NPC277721
0.6279 Remote Similarity NPC475307
0.6279 Remote Similarity NPC141769
0.6279 Remote Similarity NPC167644
0.6279 Remote Similarity NPC35164
0.6279 Remote Similarity NPC249204
0.6279 Remote Similarity NPC171741
0.6279 Remote Similarity NPC470623
0.6279 Remote Similarity NPC144790
0.6279 Remote Similarity NPC149400
0.6279 Remote Similarity NPC88962
0.6279 Remote Similarity NPC18724
0.6279 Remote Similarity NPC323231
0.6279 Remote Similarity NPC297348
0.6279 Remote Similarity NPC325828
0.6279 Remote Similarity NPC48339
0.6279 Remote Similarity NPC177834
0.6279 Remote Similarity NPC477451
0.6279 Remote Similarity NPC267266
0.6279 Remote Similarity NPC12297
0.6279 Remote Similarity NPC477547
0.6279 Remote Similarity NPC250393
0.6267 Remote Similarity NPC166250
0.6267 Remote Similarity NPC272359
0.6267 Remote Similarity NPC470151
0.6265 Remote Similarity NPC472396
0.6265 Remote Similarity NPC161928
0.6265 Remote Similarity NPC210658
0.6265 Remote Similarity NPC288952
0.625 Remote Similarity NPC472741
0.6235 Remote Similarity NPC470817
0.6235 Remote Similarity NPC223143
0.6235 Remote Similarity NPC279329
0.6235 Remote Similarity NPC65550
0.6234 Remote Similarity NPC474574
0.6234 Remote Similarity NPC64081
0.6234 Remote Similarity NPC307865
0.6234 Remote Similarity NPC143250
0.6232 Remote Similarity NPC209686
0.6232 Remote Similarity NPC236099
0.6232 Remote Similarity NPC249078
0.622 Remote Similarity NPC472442
0.622 Remote Similarity NPC119001
0.6216 Remote Similarity NPC127283
0.6216 Remote Similarity NPC197701

  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 NPC132998 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
0.7 Intermediate Similarity NPD2686 Approved
0.7 Intermediate Similarity NPD2687 Approved
0.7 Intermediate Similarity NPD2254 Approved
0.6842 Remote Similarity NPD6928 Phase 2
0.6486 Remote Similarity NPD1811 Approved
0.6486 Remote Similarity NPD1810 Approved
0.6438 Remote Similarity NPD5777 Approved
0.6418 Remote Similarity NPD1145 Discontinued
0.6286 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6279 Remote Similarity NPD8171 Discontinued
0.6184 Remote Similarity NPD3702 Approved
0.6027 Remote Similarity NPD6705 Phase 1
0.5976 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5976 Remote Similarity NPD3669 Approved
0.5972 Remote Similarity NPD4224 Phase 2
0.5946 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5946 Remote Similarity NPD4267 Clinical (unspecified phase)
0.5946 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5946 Remote Similarity NPD3698 Phase 2
0.5932 Remote Similarity NPD367 Approved
0.5926 Remote Similarity NPD1780 Approved
0.5926 Remote Similarity NPD1779 Approved
0.5867 Remote Similarity NPD4245 Approved
0.5867 Remote Similarity NPD4244 Approved
0.5867 Remote Similarity NPD4787 Phase 1
0.5867 Remote Similarity NPD4789 Approved
0.5844 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5823 Remote Similarity NPD6116 Phase 1
0.5789 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5789 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5778 Remote Similarity NPD7991 Discontinued
0.5696 Remote Similarity NPD6117 Approved
0.5645 Remote Similarity NPD385 Approved
0.5645 Remote Similarity NPD384 Approved
0.5625 Remote Similarity NPD8170 Clinical (unspecified phase)
0.56 Remote Similarity NPD5360 Phase 3
0.56 Remote Similarity NPD5361 Clinical (unspecified phase)

  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