Structure

Physi-Chem Properties

Molecular Weight:  272.25
Volume:  329.454
LogP:  6.508
LogD:  5.156
LogS:  -6.452
# 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:  0.481
Synthetic Accessibility Score:  4.481
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:  -4.653
MDCK Permeability:  1.3931691682955716e-05
Pgp-inhibitor:  0.731
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.775
30% Bioavailability (F30%):  0.115

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.77
Plasma Protein Binding (PPB):  97.33367156982422%
Volume Distribution (VD):  3.695
Pgp-substrate:  1.322342872619629%

ADMET: Metabolism

CYP1A2-inhibitor:  0.458
CYP1A2-substrate:  0.519
CYP2C19-inhibitor:  0.361
CYP2C19-substrate:  0.691
CYP2C9-inhibitor:  0.404
CYP2C9-substrate:  0.682
CYP2D6-inhibitor:  0.527
CYP2D6-substrate:  0.795
CYP3A4-inhibitor:  0.719
CYP3A4-substrate:  0.232

ADMET: Excretion

Clearance (CL):  4.998
Half-life (T1/2):  0.088

ADMET: Toxicity

hERG Blockers:  0.033
Human Hepatotoxicity (H-HT):  0.164
Drug-inuced Liver Injury (DILI):  0.294
AMES Toxicity:  0.002
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.48
Skin Sensitization:  0.965
Carcinogencity:  0.058
Eye Corrosion:  0.988
Eye Irritation:  0.951
Respiratory Toxicity:  0.066

Download Data

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

  Natural Product: NPC49088

Natural Product ID:  NPC49088
Common Name*:   (1R,3E,7E,11S,12S)-3,7,18-Dolabellatriene
IUPAC Name:   (1S,3aR,5E,9E,12aS)-3a,6,10-trimethyl-1-prop-1-en-2-yl-2,3,4,7,8,11,12,12a-octahydro-1H-cyclopenta[11]annulene
Synonyms:   (1R,3E,7E,11S,12S)-3,7,18-Dolabellatriene
Standard InCHIKey:  KZHMFCYCMBPVGZ-JFZLUAFOSA-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/h7,11,18-19H,1,6,8-10,12-14H2,2-5H3/b16-7+,17-11+/t18-,19+,20+/m1/s1
SMILES:  C=C(C)[C@H]1CC[C@]2(C)C/C=C(C)/CC/C=C(C)/CC[C@@H]12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1689074
PubChem CID:   51039832
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]
NPO29285 Dendrobium densiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29285 Dendrobium densiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29146 Polygonatum kingianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29308 Mycobacterium marinum Species Mycobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29285 Dendrobium densiflorum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29313 Halomonas meridiana Species Halomonadaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29146 Polygonatum kingianum Species Asparagaceae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 64.0 ug.mL-1 PMID[514289]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 128.0 ug.mL-1 PMID[514289]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 16.0 ug.mL-1 PMID[514289]

☑ 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 NPC49088 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 NPC323445
0.8409 Intermediate Similarity NPC473912
0.8298 Intermediate Similarity NPC178644
0.7959 Intermediate Similarity NPC200129
0.7955 Intermediate Similarity NPC246165
0.7917 Intermediate Similarity NPC124851
0.7885 Intermediate Similarity NPC470893
0.7885 Intermediate Similarity NPC123194
0.7857 Intermediate Similarity NPC92224
0.7826 Intermediate Similarity NPC51762
0.7826 Intermediate Similarity NPC90506
0.7826 Intermediate Similarity NPC60556
0.7826 Intermediate Similarity NPC141777
0.7826 Intermediate Similarity NPC86538
0.7826 Intermediate Similarity NPC227670
0.7826 Intermediate Similarity NPC166362
0.7826 Intermediate Similarity NPC474118
0.7826 Intermediate Similarity NPC23145
0.7826 Intermediate Similarity NPC90803
0.7826 Intermediate Similarity NPC109813
0.7778 Intermediate Similarity NPC469769
0.7755 Intermediate Similarity NPC22765
0.7755 Intermediate Similarity NPC17518
0.766 Intermediate Similarity NPC248411
0.7636 Intermediate Similarity NPC5698
0.7593 Intermediate Similarity NPC49575
0.7593 Intermediate Similarity NPC230823
0.7593 Intermediate Similarity NPC267626
0.7593 Intermediate Similarity NPC55004
0.75 Intermediate Similarity NPC323153
0.75 Intermediate Similarity NPC296337
0.75 Intermediate Similarity NPC86683
0.75 Intermediate Similarity NPC229403
0.75 Intermediate Similarity NPC252809
0.75 Intermediate Similarity NPC266298
0.7455 Intermediate Similarity NPC472830
0.7391 Intermediate Similarity NPC473614
0.7241 Intermediate Similarity NPC474480
0.7234 Intermediate Similarity NPC177470
0.7193 Intermediate Similarity NPC25853
0.717 Intermediate Similarity NPC127944
0.7143 Intermediate Similarity NPC266295
0.7143 Intermediate Similarity NPC30215
0.7143 Intermediate Similarity NPC241784
0.7143 Intermediate Similarity NPC114239
0.7143 Intermediate Similarity NPC94991
0.7143 Intermediate Similarity NPC13991
0.7119 Intermediate Similarity NPC140233
0.7119 Intermediate Similarity NPC287744
0.7115 Intermediate Similarity NPC471681
0.7111 Intermediate Similarity NPC297643
0.7111 Intermediate Similarity NPC229262
0.7111 Intermediate Similarity NPC139717
0.7069 Intermediate Similarity NPC210346
0.7059 Intermediate Similarity NPC17810
0.7021 Intermediate Similarity NPC144023
0.7021 Intermediate Similarity NPC120926
0.7021 Intermediate Similarity NPC218918
0.7018 Intermediate Similarity NPC309825
0.7018 Intermediate Similarity NPC259261
0.7 Intermediate Similarity NPC477009
0.7 Intermediate Similarity NPC238352
0.6949 Remote Similarity NPC474086
0.6939 Remote Similarity NPC202189
0.6909 Remote Similarity NPC469770
0.6905 Remote Similarity NPC471327
0.6897 Remote Similarity NPC234264
0.6897 Remote Similarity NPC47840
0.6889 Remote Similarity NPC76145
0.6889 Remote Similarity NPC190810
0.6889 Remote Similarity NPC34764
0.6875 Remote Similarity NPC105246
0.6875 Remote Similarity NPC190232
0.6833 Remote Similarity NPC473902
0.6833 Remote Similarity NPC309300
0.6809 Remote Similarity NPC62086
0.6809 Remote Similarity NPC78551
0.6809 Remote Similarity NPC183670
0.6809 Remote Similarity NPC227632
0.678 Remote Similarity NPC475795
0.6774 Remote Similarity NPC176107
0.6739 Remote Similarity NPC239039
0.6735 Remote Similarity NPC192529
0.6721 Remote Similarity NPC19569
0.6667 Remote Similarity NPC20610
0.6667 Remote Similarity NPC160209
0.6667 Remote Similarity NPC282119
0.6667 Remote Similarity NPC11130
0.6667 Remote Similarity NPC103290
0.6667 Remote Similarity NPC124112
0.6667 Remote Similarity NPC278550
0.6667 Remote Similarity NPC165695
0.6613 Remote Similarity NPC176171
0.6613 Remote Similarity NPC92327
0.661 Remote Similarity NPC135648
0.661 Remote Similarity NPC471081
0.6604 Remote Similarity NPC26960
0.6604 Remote Similarity NPC329773
0.6604 Remote Similarity NPC182102
0.6562 Remote Similarity NPC182815
0.6562 Remote Similarity NPC167272
0.6562 Remote Similarity NPC269877
0.6562 Remote Similarity NPC469677
0.6562 Remote Similarity NPC22301
0.6557 Remote Similarity NPC475704
0.6545 Remote Similarity NPC476679
0.6531 Remote Similarity NPC193180
0.6512 Remote Similarity NPC206088
0.6512 Remote Similarity NPC66577
0.6512 Remote Similarity NPC151719
0.65 Remote Similarity NPC213152
0.65 Remote Similarity NPC274704
0.6462 Remote Similarity NPC9161
0.6462 Remote Similarity NPC159577
0.6462 Remote Similarity NPC214770
0.6462 Remote Similarity NPC475728
0.6462 Remote Similarity NPC49422
0.6462 Remote Similarity NPC477856
0.6462 Remote Similarity NPC35734
0.6462 Remote Similarity NPC282593
0.6452 Remote Similarity NPC187619
0.6452 Remote Similarity NPC183422
0.6441 Remote Similarity NPC469321
0.6429 Remote Similarity NPC95581
0.6429 Remote Similarity NPC123965
0.6429 Remote Similarity NPC115959
0.6393 Remote Similarity NPC279200
0.6383 Remote Similarity NPC48638
0.6383 Remote Similarity NPC45727
0.6379 Remote Similarity NPC474457
0.6379 Remote Similarity NPC474415
0.6379 Remote Similarity NPC474528
0.6379 Remote Similarity NPC475696
0.6364 Remote Similarity NPC213749
0.6364 Remote Similarity NPC471662
0.6364 Remote Similarity NPC21773
0.6364 Remote Similarity NPC470078
0.6364 Remote Similarity NPC115023
0.6364 Remote Similarity NPC471660
0.6349 Remote Similarity NPC135650
0.6349 Remote Similarity NPC162309
0.6333 Remote Similarity NPC176621
0.629 Remote Similarity NPC212210
0.6271 Remote Similarity NPC60772
0.6269 Remote Similarity NPC470044
0.6269 Remote Similarity NPC474140
0.6269 Remote Similarity NPC474228
0.6269 Remote Similarity NPC470045
0.6269 Remote Similarity NPC303613
0.6269 Remote Similarity NPC251705
0.625 Remote Similarity NPC136813
0.623 Remote Similarity NPC63111
0.623 Remote Similarity NPC60565
0.623 Remote Similarity NPC219621
0.623 Remote Similarity NPC97322
0.6212 Remote Similarity NPC40574
0.6212 Remote Similarity NPC307176
0.6182 Remote Similarity NPC27438
0.6176 Remote Similarity NPC329090
0.6176 Remote Similarity NPC471659
0.6176 Remote Similarity NPC476904
0.6176 Remote Similarity NPC309852
0.6176 Remote Similarity NPC27395
0.6167 Remote Similarity NPC474420
0.6167 Remote Similarity NPC474454
0.6167 Remote Similarity NPC143834
0.6167 Remote Similarity NPC474455
0.6167 Remote Similarity NPC475716
0.6154 Remote Similarity NPC167527
0.6154 Remote Similarity NPC224532
0.6154 Remote Similarity NPC469688
0.6136 Remote Similarity NPC100879
0.6136 Remote Similarity NPC3649
0.6129 Remote Similarity NPC283247
0.6129 Remote Similarity NPC211291
0.6129 Remote Similarity NPC32285
0.6129 Remote Similarity NPC133368
0.6119 Remote Similarity NPC265789
0.6119 Remote Similarity NPC181204
0.6119 Remote Similarity NPC234707
0.6111 Remote Similarity NPC106990
0.6094 Remote Similarity NPC272125
0.6094 Remote Similarity NPC323005
0.6087 Remote Similarity NPC136188
0.6087 Remote Similarity NPC182392
0.6087 Remote Similarity NPC162742
0.6087 Remote Similarity NPC230301
0.6087 Remote Similarity NPC251435
0.6087 Remote Similarity NPC257347
0.6087 Remote Similarity NPC134847
0.6087 Remote Similarity NPC125828
0.6087 Remote Similarity NPC304309
0.6087 Remote Similarity NPC22105
0.6087 Remote Similarity NPC285893
0.6087 Remote Similarity NPC113639
0.6087 Remote Similarity NPC28657
0.6087 Remote Similarity NPC141071
0.6087 Remote Similarity NPC471468
0.6087 Remote Similarity NPC319090
0.6087 Remote Similarity NPC328104

  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 NPC49088 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
0.7059 Intermediate Similarity NPD8262 Approved
0.6889 Remote Similarity NPD319 Phase 1
0.6875 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6562 Remote Similarity NPD6922 Approved
0.6562 Remote Similarity NPD6923 Approved
0.6462 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6462 Remote Similarity NPD6939 Phase 2
0.6462 Remote Similarity NPD7143 Approved
0.6462 Remote Similarity NPD7144 Approved
0.6364 Remote Similarity NPD7152 Approved
0.6364 Remote Similarity NPD7150 Approved
0.6364 Remote Similarity NPD4243 Approved
0.6364 Remote Similarity NPD7151 Approved
0.6212 Remote Similarity NPD4747 Approved
0.6176 Remote Similarity NPD4784 Approved
0.6176 Remote Similarity NPD6924 Approved
0.6176 Remote Similarity NPD4785 Approved
0.6176 Remote Similarity NPD6926 Approved
0.6176 Remote Similarity NPD5733 Approved
0.6154 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6119 Remote Similarity NPD5276 Approved
0.6087 Remote Similarity NPD6942 Approved
0.6087 Remote Similarity NPD7339 Approved
0.6061 Remote Similarity NPD4137 Phase 3
0.6 Remote Similarity NPD6933 Approved
0.597 Remote Similarity NPD4691 Approved
0.5942 Remote Similarity NPD4687 Approved
0.5932 Remote Similarity NPD4219 Approved
0.5915 Remote Similarity NPD6932 Approved
0.5915 Remote Similarity NPD5776 Phase 2
0.5915 Remote Similarity NPD6925 Approved
0.5857 Remote Similarity NPD4190 Phase 3
0.5857 Remote Similarity NPD5275 Approved
0.5833 Remote Similarity NPD7145 Approved
0.5753 Remote Similarity NPD6683 Phase 2
0.5753 Remote Similarity NPD6929 Approved
0.5714 Remote Similarity NPD4058 Approved
0.5676 Remote Similarity NPD6930 Phase 2
0.5676 Remote Similarity NPD7514 Phase 3
0.5676 Remote Similarity NPD7525 Registered
0.5676 Remote Similarity NPD6931 Approved
0.5616 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5616 Remote Similarity NPD7322 Clinical (unspecified phase)
0.56 Remote Similarity NPD6902 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