Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  329.454
LogP:  6.756
LogD:  5.428
LogS:  -6.667
# Rotatable Bonds:  1
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.491
Synthetic Accessibility Score:  4.792
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.667
MDCK Permeability:  2.537020918680355e-05
Pgp-inhibitor:  0.894
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.514
30% Bioavailability (F30%):  0.064

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.13
Plasma Protein Binding (PPB):  93.34850311279297%
Volume Distribution (VD):  3.511
Pgp-substrate:  2.297327756881714%

ADMET: Metabolism

CYP1A2-inhibitor:  0.504
CYP1A2-substrate:  0.69
CYP2C19-inhibitor:  0.444
CYP2C19-substrate:  0.928
CYP2C9-inhibitor:  0.42
CYP2C9-substrate:  0.437
CYP2D6-inhibitor:  0.926
CYP2D6-substrate:  0.389
CYP3A4-inhibitor:  0.946
CYP3A4-substrate:  0.465

ADMET: Excretion

Clearance (CL):  3.356
Half-life (T1/2):  0.1

ADMET: Toxicity

hERG Blockers:  0.077
Human Hepatotoxicity (H-HT):  0.286
Drug-inuced Liver Injury (DILI):  0.166
AMES Toxicity:  0.004
Rat Oral Acute Toxicity:  0.149
Maximum Recommended Daily Dose:  0.978
Skin Sensitization:  0.958
Carcinogencity:  0.046
Eye Corrosion:  0.535
Eye Irritation:  0.875
Respiratory Toxicity:  0.078

Download Data

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

  Natural Product: NPC323445

Natural Product ID:  NPC323445
Common Name*:   (1R,2E,4R,7E,11S,12R)-2,7,18-Dolabellatriene
IUPAC Name:   (1R,3aR,4E,6R,9E,12aS)-3a,6,10-trimethyl-1-prop-1-en-2-yl-2,3,6,7,8,11,12,12a-octahydro-1H-cyclopenta[11]annulene
Synonyms:   (1R,2E,4R,7E,11S,12R)-2,7,18-Dolabellatriene
Standard InCHIKey:  DQSHCYDPVQKJSC-IAGGUBJBSA-N
Standard InCHI:  InChI=1S/C20H32/c1-15(2)18-12-14-20(5)13-11-17(4)8-6-7-16(3)9-10-19(18)20/h7,11,13,17-19H,1,6,8-10,12,14H2,2-5H3/b13-11+,16-7+/t17-,18+,19+,20+/m1/s1
SMILES:  C[C@@H]1CC/C=C(C)/CC[C@@H]2[C@](/C=C/1)(C)CC[C@H]2C(=C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1689085
PubChem CID:   51040259
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001760] Dolabellane and neodolabellane 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
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. at a depth of 0.1-1 m, Elafonissos Island (3630' N, 2258' E), south of Peloponnese, Greece 2004-APR PMID[21190330]
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. n.a. n.a. PMID[21190330]
NPO31140 Dilophus spiralis Species Dictyotaceae Eukaryota n.a. Elafonissos Island (GPS coordinates 3630' N, 2258' E), south of Peloponnese, Greece 2004-APR PMID[21190330]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 128.0 ug.mL-1 PMID[529327]

☑ 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 NPC323445 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
0.9767 High Similarity NPC49088
0.8511 High Similarity NPC178644
0.8222 Intermediate Similarity NPC473912
0.8125 Intermediate Similarity NPC124851
0.8077 Intermediate Similarity NPC470893
0.7963 Intermediate Similarity NPC469769
0.78 Intermediate Similarity NPC200129
0.7778 Intermediate Similarity NPC246165
0.7736 Intermediate Similarity NPC123194
0.7679 Intermediate Similarity NPC323153
0.7674 Intermediate Similarity NPC92224
0.766 Intermediate Similarity NPC51762
0.766 Intermediate Similarity NPC60556
0.766 Intermediate Similarity NPC23145
0.766 Intermediate Similarity NPC109813
0.766 Intermediate Similarity NPC166362
0.766 Intermediate Similarity NPC90506
0.766 Intermediate Similarity NPC227670
0.766 Intermediate Similarity NPC86538
0.766 Intermediate Similarity NPC141777
0.766 Intermediate Similarity NPC90803
0.766 Intermediate Similarity NPC474118
0.76 Intermediate Similarity NPC22765
0.76 Intermediate Similarity NPC17518
0.75 Intermediate Similarity NPC5698
0.75 Intermediate Similarity NPC248411
0.7455 Intermediate Similarity NPC55004
0.7455 Intermediate Similarity NPC230823
0.7455 Intermediate Similarity NPC49575
0.7455 Intermediate Similarity NPC267626
0.7447 Intermediate Similarity NPC177470
0.7368 Intermediate Similarity NPC252809
0.7347 Intermediate Similarity NPC86683
0.7347 Intermediate Similarity NPC229403
0.7347 Intermediate Similarity NPC296337
0.7333 Intermediate Similarity NPC266298
0.7321 Intermediate Similarity NPC472830
0.7255 Intermediate Similarity NPC17810
0.7234 Intermediate Similarity NPC120926
0.7234 Intermediate Similarity NPC218918
0.7234 Intermediate Similarity NPC144023
0.7234 Intermediate Similarity NPC473614
0.7119 Intermediate Similarity NPC474480
0.7119 Intermediate Similarity NPC474086
0.7083 Intermediate Similarity NPC105246
0.7083 Intermediate Similarity NPC190232
0.7069 Intermediate Similarity NPC25853
0.7037 Intermediate Similarity NPC127944
0.7021 Intermediate Similarity NPC183670
0.7018 Intermediate Similarity NPC94991
0.7018 Intermediate Similarity NPC266295
0.7018 Intermediate Similarity NPC30215
0.7 Intermediate Similarity NPC140233
0.7 Intermediate Similarity NPC114239
0.7 Intermediate Similarity NPC287744
0.7 Intermediate Similarity NPC241784
0.7 Intermediate Similarity NPC13991
0.6981 Remote Similarity NPC471681
0.6957 Remote Similarity NPC229262
0.6957 Remote Similarity NPC139717
0.6957 Remote Similarity NPC297643
0.6949 Remote Similarity NPC210346
0.6935 Remote Similarity NPC176107
0.6897 Remote Similarity NPC259261
0.6897 Remote Similarity NPC309825
0.6889 Remote Similarity NPC282119
0.6885 Remote Similarity NPC238352
0.6885 Remote Similarity NPC477009
0.68 Remote Similarity NPC202189
0.6786 Remote Similarity NPC469770
0.678 Remote Similarity NPC47840
0.678 Remote Similarity NPC234264
0.6774 Remote Similarity NPC176171
0.6774 Remote Similarity NPC92327
0.6744 Remote Similarity NPC206088
0.6744 Remote Similarity NPC151719
0.6744 Remote Similarity NPC66577
0.6744 Remote Similarity NPC471327
0.6739 Remote Similarity NPC34764
0.6739 Remote Similarity NPC76145
0.6739 Remote Similarity NPC190810
0.6727 Remote Similarity NPC476679
0.6721 Remote Similarity NPC309300
0.6721 Remote Similarity NPC473902
0.6719 Remote Similarity NPC182815
0.6667 Remote Similarity NPC62086
0.6667 Remote Similarity NPC78551
0.6667 Remote Similarity NPC227632
0.6667 Remote Similarity NPC475795
0.6615 Remote Similarity NPC475728
0.6615 Remote Similarity NPC9161
0.6615 Remote Similarity NPC49422
0.6613 Remote Similarity NPC19569
0.66 Remote Similarity NPC192529
0.6596 Remote Similarity NPC239039
0.6596 Remote Similarity NPC48638
0.6596 Remote Similarity NPC45727
0.6562 Remote Similarity NPC20610
0.6562 Remote Similarity NPC160209
0.6557 Remote Similarity NPC165695
0.6557 Remote Similarity NPC124112
0.6552 Remote Similarity NPC278550
0.6552 Remote Similarity NPC11130
0.6531 Remote Similarity NPC103290
0.6515 Remote Similarity NPC115023
0.6515 Remote Similarity NPC471660
0.6515 Remote Similarity NPC470078
0.65 Remote Similarity NPC176621
0.65 Remote Similarity NPC471081
0.65 Remote Similarity NPC135648
0.6481 Remote Similarity NPC26960
0.6481 Remote Similarity NPC329773
0.6481 Remote Similarity NPC182102
0.6462 Remote Similarity NPC269877
0.6462 Remote Similarity NPC469677
0.6462 Remote Similarity NPC22301
0.6462 Remote Similarity NPC167272
0.6452 Remote Similarity NPC475704
0.6441 Remote Similarity NPC60772
0.6418 Remote Similarity NPC470045
0.6418 Remote Similarity NPC251705
0.6418 Remote Similarity NPC470044
0.64 Remote Similarity NPC193180
0.6393 Remote Similarity NPC213152
0.6393 Remote Similarity NPC274704
0.6364 Remote Similarity NPC40574
0.6364 Remote Similarity NPC214770
0.6364 Remote Similarity NPC477856
0.6364 Remote Similarity NPC35734
0.6364 Remote Similarity NPC282593
0.6364 Remote Similarity NPC159577
0.6349 Remote Similarity NPC187619
0.6349 Remote Similarity NPC183422
0.6333 Remote Similarity NPC469321
0.6324 Remote Similarity NPC309852
0.6316 Remote Similarity NPC95581
0.6304 Remote Similarity NPC182392
0.629 Remote Similarity NPC283247
0.629 Remote Similarity NPC279200
0.6279 Remote Similarity NPC123965
0.6279 Remote Similarity NPC115959
0.6279 Remote Similarity NPC34671
0.6271 Remote Similarity NPC474415
0.6271 Remote Similarity NPC474528
0.6271 Remote Similarity NPC474457
0.6271 Remote Similarity NPC475696
0.6269 Remote Similarity NPC234707
0.6269 Remote Similarity NPC181204
0.6269 Remote Similarity NPC471662
0.6269 Remote Similarity NPC21773
0.625 Remote Similarity NPC162309
0.625 Remote Similarity NPC135650
0.625 Remote Similarity NPC323005
0.6232 Remote Similarity NPC113639
0.6232 Remote Similarity NPC471468
0.6232 Remote Similarity NPC293803
0.6222 Remote Similarity NPC213749
0.619 Remote Similarity NPC212210
0.6176 Remote Similarity NPC303613
0.6176 Remote Similarity NPC474228
0.6176 Remote Similarity NPC474140
0.6167 Remote Similarity NPC10017
0.6154 Remote Similarity NPC136813
0.6143 Remote Similarity NPC69408
0.6143 Remote Similarity NPC129165
0.6143 Remote Similarity NPC310643
0.6143 Remote Similarity NPC113733
0.6143 Remote Similarity NPC474463
0.6143 Remote Similarity NPC470362
0.6143 Remote Similarity NPC134330
0.614 Remote Similarity NPC165755
0.614 Remote Similarity NPC14002
0.6129 Remote Similarity NPC60565
0.6129 Remote Similarity NPC97322
0.6129 Remote Similarity NPC469728
0.6129 Remote Similarity NPC219621
0.6129 Remote Similarity NPC63111
0.6119 Remote Similarity NPC307176
0.6102 Remote Similarity NPC249645
0.6102 Remote Similarity NPC55412
0.6087 Remote Similarity NPC476904
0.6087 Remote Similarity NPC305759
0.6087 Remote Similarity NPC27395
0.6087 Remote Similarity NPC99088
0.6087 Remote Similarity NPC471659
0.6087 Remote Similarity NPC329090
0.6087 Remote Similarity NPC329866
0.6087 Remote Similarity NPC173592
0.6087 Remote Similarity NPC474797
0.6087 Remote Similarity NPC474796
0.6071 Remote Similarity NPC27438
0.6066 Remote Similarity NPC474455
0.6066 Remote Similarity NPC475716
0.6066 Remote Similarity NPC474420
0.6066 Remote Similarity NPC143834
0.6066 Remote Similarity NPC474454
0.6061 Remote Similarity NPC224532
0.6061 Remote Similarity NPC469688
0.6061 Remote Similarity NPC167527
0.6056 Remote Similarity NPC474230

  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 NPC323445 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
0.7255 Intermediate Similarity NPD8262 Approved
0.7083 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6739 Remote Similarity NPD319 Phase 1
0.6615 Remote Similarity NPD7143 Approved
0.6615 Remote Similarity NPD7144 Approved
0.6515 Remote Similarity NPD7150 Approved
0.6515 Remote Similarity NPD7151 Approved
0.6515 Remote Similarity NPD7152 Approved
0.6462 Remote Similarity NPD6922 Approved
0.6462 Remote Similarity NPD6923 Approved
0.6364 Remote Similarity NPD6939 Phase 2
0.6364 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6324 Remote Similarity NPD4785 Approved
0.6324 Remote Similarity NPD4784 Approved
0.6269 Remote Similarity NPD4243 Approved
0.6119 Remote Similarity NPD4747 Approved
0.6102 Remote Similarity NPD4219 Approved
0.6087 Remote Similarity NPD4687 Approved
0.6087 Remote Similarity NPD6926 Approved
0.6087 Remote Similarity NPD5733 Approved
0.6087 Remote Similarity NPD6924 Approved
0.6061 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6056 Remote Similarity NPD6932 Approved
0.6029 Remote Similarity NPD5276 Approved
0.6 Remote Similarity NPD7339 Approved
0.6 Remote Similarity NPD6942 Approved
0.5972 Remote Similarity NPD7145 Approved
0.597 Remote Similarity NPD4137 Phase 3
0.5915 Remote Similarity NPD6933 Approved
0.5882 Remote Similarity NPD4691 Approved
0.5857 Remote Similarity NPD4058 Approved
0.5833 Remote Similarity NPD6925 Approved
0.5833 Remote Similarity NPD5776 Phase 2
0.5811 Remote Similarity NPD7514 Phase 3
0.5775 Remote Similarity NPD5275 Approved
0.5775 Remote Similarity NPD4190 Phase 3
0.5753 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5753 Remote Similarity NPD7322 Clinical (unspecified phase)
0.5735 Remote Similarity NPD1673 Approved
0.5733 Remote Similarity NPD6902 Approved
0.5692 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5676 Remote Similarity NPD6929 Approved
0.5676 Remote Similarity NPD6683 Phase 2
0.5676 Remote Similarity NPD4195 Approved
0.5625 Remote Similarity NPD4194 Approved
0.5625 Remote Similarity NPD4193 Approved
0.5625 Remote Similarity NPD4191 Approved
0.5625 Remote Similarity NPD4192 Approved
0.56 Remote Similarity NPD6930 Phase 2
0.56 Remote Similarity NPD6931 Approved
0.56 Remote Similarity NPD7332 Phase 2
0.56 Remote Similarity NPD7525 Registered

  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