Structure

Physi-Chem Properties

Molecular Weight:  254.19
Volume:  268.698
LogP:  2.749
LogD:  2.258
LogS:  -3.698
# Rotatable Bonds:  1
TPSA:  52.99
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.705
Synthetic Accessibility Score:  4.785
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.64
MDCK Permeability:  3.086045398958959e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.035
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.119
30% Bioavailability (F30%):  0.058

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.432
Plasma Protein Binding (PPB):  67.49686431884766%
Volume Distribution (VD):  1.458
Pgp-substrate:  26.245508193969727%

ADMET: Metabolism

CYP1A2-inhibitor:  0.025
CYP1A2-substrate:  0.499
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.86
CYP2C9-inhibitor:  0.045
CYP2C9-substrate:  0.096
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.492
CYP3A4-inhibitor:  0.112
CYP3A4-substrate:  0.196

ADMET: Excretion

Clearance (CL):  6.016
Half-life (T1/2):  0.539

ADMET: Toxicity

hERG Blockers:  0.212
Human Hepatotoxicity (H-HT):  0.832
Drug-inuced Liver Injury (DILI):  0.118
AMES Toxicity:  0.045
Rat Oral Acute Toxicity:  0.938
Maximum Recommended Daily Dose:  0.678
Skin Sensitization:  0.628
Carcinogencity:  0.04
Eye Corrosion:  0.354
Eye Irritation:  0.9
Respiratory Toxicity:  0.969

Download Data

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

  Natural Product: NPC165069

Natural Product ID:  NPC165069
Common Name*:   Trichocarane A
IUPAC Name:   (1aS,2aR,4S,5R,5aR,7aR)-2a,7a-dimethyl-5-propan-2-yl-2,3,4,5a,6,7-hexahydro-1aH-azuleno[5,6-b]oxirene-4,5-diol
Synonyms:  
Standard InCHIKey:  KZIYMGXPOZNBKF-YXJLRHLOSA-N
Standard InCHI:  InChI=1S/C15H26O3/c1-9(2)15(17)10-5-6-14(4)12(18-14)8-13(10,3)7-11(15)16/h9-12,16-17H,5-8H2,1-4H3/t10-,11+,12+,13-,14-,15-/m1/s1
SMILES:  CC(C)[C@]1([C@@H]2CC[C@]3(C)[C@H](C[C@@]2(C)C[C@@H]1O)O3)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL443704
PubChem CID:   21606643
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001670] Tertiary alcohols

*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
NPO13533 Trichoderma virens Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[11000018]
NPO13533 Trichoderma virens Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[12662106]
NPO13533 Trichoderma virens Species Hypocreaceae Eukaryota n.a. n.a. n.a. PMID[31418264]
NPO13533 Trichoderma virens Species Hypocreaceae 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
NPT119 Organism Triticum aestivum Triticum aestivum Inhibition = 40.0 % PMID[573855]

☑ 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 NPC165069 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
0.9167 High Similarity NPC475968
0.8889 High Similarity NPC199937
0.8226 Intermediate Similarity NPC291147
0.7937 Intermediate Similarity NPC119425
0.7903 Intermediate Similarity NPC45387
0.7867 Intermediate Similarity NPC117137
0.7867 Intermediate Similarity NPC66766
0.7763 Intermediate Similarity NPC473257
0.7467 Intermediate Similarity NPC188793
0.7463 Intermediate Similarity NPC475807
0.7436 Intermediate Similarity NPC212340
0.7397 Intermediate Similarity NPC470659
0.7397 Intermediate Similarity NPC470660
0.7342 Intermediate Similarity NPC260852
0.7313 Intermediate Similarity NPC475412
0.7286 Intermediate Similarity NPC469328
0.726 Intermediate Similarity NPC41886
0.7246 Intermediate Similarity NPC476702
0.7237 Intermediate Similarity NPC476233
0.7213 Intermediate Similarity NPC127997
0.7213 Intermediate Similarity NPC95969
0.7206 Intermediate Similarity NPC172622
0.72 Intermediate Similarity NPC131584
0.72 Intermediate Similarity NPC139765
0.7125 Intermediate Similarity NPC29342
0.7125 Intermediate Similarity NPC2572
0.7105 Intermediate Similarity NPC126969
0.7105 Intermediate Similarity NPC470145
0.7105 Intermediate Similarity NPC279575
0.7101 Intermediate Similarity NPC236099
0.7101 Intermediate Similarity NPC209686
0.7101 Intermediate Similarity NPC249078
0.7089 Intermediate Similarity NPC216941
0.7077 Intermediate Similarity NPC166894
0.7077 Intermediate Similarity NPC89069
0.7077 Intermediate Similarity NPC277917
0.7077 Intermediate Similarity NPC178223
0.7077 Intermediate Similarity NPC283655
0.7073 Intermediate Similarity NPC64862
0.7051 Intermediate Similarity NPC170595
0.7013 Intermediate Similarity NPC83108
0.7013 Intermediate Similarity NPC214030
0.7 Intermediate Similarity NPC475849
0.6962 Remote Similarity NPC16449
0.6933 Remote Similarity NPC153719
0.6933 Remote Similarity NPC248427
0.6914 Remote Similarity NPC474266
0.6914 Remote Similarity NPC471340
0.6914 Remote Similarity NPC69953
0.6901 Remote Similarity NPC190827
0.6901 Remote Similarity NPC475943
0.6901 Remote Similarity NPC243469
0.6866 Remote Similarity NPC322148
0.6866 Remote Similarity NPC150713
0.6866 Remote Similarity NPC29976
0.6849 Remote Similarity NPC474756
0.6842 Remote Similarity NPC475458
0.6842 Remote Similarity NPC48795
0.6835 Remote Similarity NPC287452
0.6829 Remote Similarity NPC474156
0.68 Remote Similarity NPC8004
0.68 Remote Similarity NPC127283
0.6795 Remote Similarity NPC185915
0.6795 Remote Similarity NPC471454
0.679 Remote Similarity NPC475388
0.6753 Remote Similarity NPC472950
0.6753 Remote Similarity NPC231680
0.6753 Remote Similarity NPC91387
0.6753 Remote Similarity NPC270306
0.6753 Remote Similarity NPC472952
0.6753 Remote Similarity NPC317242
0.6719 Remote Similarity NPC474331
0.6714 Remote Similarity NPC185547
0.6714 Remote Similarity NPC95804
0.6712 Remote Similarity NPC63190
0.6711 Remote Similarity NPC470610
0.6709 Remote Similarity NPC18857
0.6709 Remote Similarity NPC67657
0.6709 Remote Similarity NPC471769
0.6706 Remote Similarity NPC22376
0.6667 Remote Similarity NPC471781
0.6667 Remote Similarity NPC52431
0.6667 Remote Similarity NPC99480
0.6667 Remote Similarity NPC471661
0.6667 Remote Similarity NPC163597
0.6667 Remote Similarity NPC184049
0.6667 Remote Similarity NPC472946
0.6667 Remote Similarity NPC474699
0.6667 Remote Similarity NPC310228
0.6628 Remote Similarity NPC228059
0.6625 Remote Similarity NPC269333
0.6588 Remote Similarity NPC5943
0.6582 Remote Similarity NPC128951
0.6582 Remote Similarity NPC192046
0.6582 Remote Similarity NPC11907
0.6582 Remote Similarity NPC474574
0.6582 Remote Similarity NPC477227
0.6582 Remote Similarity NPC302578
0.6582 Remote Similarity NPC105208
0.6582 Remote Similarity NPC64081
0.6582 Remote Similarity NPC133596
0.6579 Remote Similarity NPC195530
0.6579 Remote Similarity NPC1340
0.6579 Remote Similarity NPC470071
0.6579 Remote Similarity NPC187471
0.6579 Remote Similarity NPC157777
0.6579 Remote Similarity NPC131506
0.6579 Remote Similarity NPC252182
0.6548 Remote Similarity NPC266651
0.6538 Remote Similarity NPC186851
0.6533 Remote Similarity NPC299948
0.6533 Remote Similarity NPC241085
0.6533 Remote Similarity NPC477820
0.6533 Remote Similarity NPC470830
0.6533 Remote Similarity NPC98711
0.6533 Remote Similarity NPC475062
0.6517 Remote Similarity NPC39453
0.6515 Remote Similarity NPC161473
0.6506 Remote Similarity NPC259173
0.65 Remote Similarity NPC471045
0.6494 Remote Similarity NPC473238
0.6494 Remote Similarity NPC472341
0.6486 Remote Similarity NPC33583
0.6486 Remote Similarity NPC161612
0.6477 Remote Similarity NPC59006
0.6477 Remote Similarity NPC473066
0.6471 Remote Similarity NPC472745
0.6471 Remote Similarity NPC474448
0.6471 Remote Similarity NPC131365
0.6471 Remote Similarity NPC145245
0.6463 Remote Similarity NPC77311
0.6447 Remote Similarity NPC63588
0.6447 Remote Similarity NPC251201
0.6447 Remote Similarity NPC254845
0.6447 Remote Similarity NPC232925
0.6438 Remote Similarity NPC300442
0.6429 Remote Similarity NPC242016
0.6429 Remote Similarity NPC291310
0.6429 Remote Similarity NPC227260
0.6429 Remote Similarity NPC9880
0.6429 Remote Similarity NPC230070
0.6429 Remote Similarity NPC87828
0.642 Remote Similarity NPC81074
0.642 Remote Similarity NPC477282
0.642 Remote Similarity NPC476176
0.641 Remote Similarity NPC470151
0.641 Remote Similarity NPC304499
0.641 Remote Similarity NPC472944
0.641 Remote Similarity NPC215030
0.641 Remote Similarity NPC471659
0.641 Remote Similarity NPC10476
0.641 Remote Similarity NPC192501
0.641 Remote Similarity NPC477508
0.641 Remote Similarity NPC228994
0.641 Remote Similarity NPC472945
0.641 Remote Similarity NPC470630
0.6395 Remote Similarity NPC210658
0.6395 Remote Similarity NPC161928
0.6395 Remote Similarity NPC472396
0.6389 Remote Similarity NPC50435
0.6386 Remote Similarity NPC470611
0.6375 Remote Similarity NPC474404
0.6375 Remote Similarity NPC171658
0.6375 Remote Similarity NPC186109
0.6364 Remote Similarity NPC473279
0.6364 Remote Similarity NPC470832
0.6364 Remote Similarity NPC197107
0.6353 Remote Similarity NPC232044
0.6353 Remote Similarity NPC273290
0.6341 Remote Similarity NPC257296
0.6341 Remote Similarity NPC472951
0.6341 Remote Similarity NPC472943
0.6341 Remote Similarity NPC474714
0.6341 Remote Similarity NPC248944
0.6341 Remote Similarity NPC7479
0.6341 Remote Similarity NPC156658
0.6341 Remote Similarity NPC258965
0.6341 Remote Similarity NPC186588
0.6338 Remote Similarity NPC66145
0.6333 Remote Similarity NPC30687
0.6333 Remote Similarity NPC470424
0.6329 Remote Similarity NPC243027
0.6329 Remote Similarity NPC158208
0.6329 Remote Similarity NPC196136
0.6322 Remote Similarity NPC470009
0.6322 Remote Similarity NPC128475
0.6316 Remote Similarity NPC66407
0.6316 Remote Similarity NPC254037
0.6316 Remote Similarity NPC144647
0.6316 Remote Similarity NPC107919
0.6316 Remote Similarity NPC129829
0.631 Remote Similarity NPC478054
0.631 Remote Similarity NPC470070
0.6301 Remote Similarity NPC167995
0.6301 Remote Similarity NPC159654
0.6301 Remote Similarity NPC281540
0.6301 Remote Similarity NPC118937
0.6301 Remote Similarity NPC219940
0.6296 Remote Similarity NPC147993
0.6292 Remote Similarity NPC36372

  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 NPC165069 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
0.6341 Remote Similarity NPD6928 Phase 2
0.6316 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6301 Remote Similarity NPD371 Approved
0.6234 Remote Similarity NPD4787 Phase 1
0.5972 Remote Similarity NPD3198 Approved
0.5938 Remote Similarity NPD388 Approved
0.5938 Remote Similarity NPD386 Approved
0.5926 Remote Similarity NPD3702 Approved
0.5897 Remote Similarity NPD3698 Phase 2
0.587 Remote Similarity NPD8171 Discontinued
0.5854 Remote Similarity NPD6933 Approved
0.5846 Remote Similarity NPD385 Approved
0.5846 Remote Similarity NPD384 Approved
0.5843 Remote Similarity NPD7524 Approved
0.5823 Remote Similarity NPD4245 Approved
0.5823 Remote Similarity NPD4244 Approved
0.5789 Remote Similarity NPD3171 Clinical (unspecified phase)
0.5747 Remote Similarity NPD6695 Phase 3
0.5682 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5612 Remote Similarity NPD1700 Approved
0.561 Remote Similarity NPD1811 Approved
0.561 Remote Similarity NPD6924 Approved
0.561 Remote Similarity NPD1810 Approved
0.561 Remote Similarity NPD6926 Approved
0.56 Remote Similarity NPD4056 Clinical (unspecified phase)
0.56 Remote Similarity NPD4057 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