Structure

Physi-Chem Properties

Molecular Weight:  256.2
Volume:  277.254
LogP:  2.206
LogD:  1.953
LogS:  -3.011
# Rotatable Bonds:  2
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.707
Synthetic Accessibility Score:  4.281
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:  -4.483
MDCK Permeability:  9.59616318141343e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.349
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.005

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.816
Plasma Protein Binding (PPB):  66.10893249511719%
Volume Distribution (VD):  0.893
Pgp-substrate:  34.51101303100586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.027
CYP1A2-substrate:  0.405
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.826
CYP2C9-inhibitor:  0.024
CYP2C9-substrate:  0.144
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.16
CYP3A4-inhibitor:  0.089
CYP3A4-substrate:  0.134

ADMET: Excretion

Clearance (CL):  5.902
Half-life (T1/2):  0.508

ADMET: Toxicity

hERG Blockers:  0.077
Human Hepatotoxicity (H-HT):  0.578
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.007
Rat Oral Acute Toxicity:  0.839
Maximum Recommended Daily Dose:  0.874
Skin Sensitization:  0.658
Carcinogencity:  0.033
Eye Corrosion:  0.055
Eye Irritation:  0.532
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC475968

Natural Product ID:  NPC475968
Common Name*:   Trichocarane C
IUPAC Name:   (1R,2S,3aS,8aR)-6-(hydroxymethyl)-3a-methyl-1-propan-2-yl-2,3,4,5,6,7,8,8a-octahydroazulene-1,2-diol
Synonyms:   3Beta,4Beta,14-Trihydroxycarotane
Standard InCHIKey:  WTQQWFFTXHFCPX-KIAMUWECSA-N
Standard InCHI:  InChI=1S/C15H28O3/c1-10(2)15(18)12-5-4-11(9-16)6-7-14(12,3)8-13(15)17/h10-13,16-18H,4-9H2,1-3H3/t11?,12-,13+,14+,15-/m1/s1
SMILES:  OCC1CC[C@@H]2[C@](CC1)(C)C[C@@H]([C@@]2(O)C(C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL519866
PubChem CID:   10563048
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

*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 = 86.0 % PMID[479484]

☑ 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 NPC475968 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 NPC165069
0.8621 High Similarity NPC119425
0.8621 High Similarity NPC291147
0.8387 Intermediate Similarity NPC199937
0.8276 Intermediate Similarity NPC45387
0.7794 Intermediate Similarity NPC41886
0.7714 Intermediate Similarity NPC139765
0.7714 Intermediate Similarity NPC131584
0.7667 Intermediate Similarity NPC283655
0.7667 Intermediate Similarity NPC178223
0.7667 Intermediate Similarity NPC166894
0.7667 Intermediate Similarity NPC277917
0.7667 Intermediate Similarity NPC89069
0.7656 Intermediate Similarity NPC249078
0.7656 Intermediate Similarity NPC209686
0.7656 Intermediate Similarity NPC236099
0.7606 Intermediate Similarity NPC126969
0.7544 Intermediate Similarity NPC95969
0.7544 Intermediate Similarity NPC127997
0.7429 Intermediate Similarity NPC153719
0.7424 Intermediate Similarity NPC243469
0.7424 Intermediate Similarity NPC190827
0.7424 Intermediate Similarity NPC475943
0.7419 Intermediate Similarity NPC150713
0.7419 Intermediate Similarity NPC29976
0.7353 Intermediate Similarity NPC474756
0.7344 Intermediate Similarity NPC475412
0.7324 Intermediate Similarity NPC48795
0.726 Intermediate Similarity NPC185915
0.7231 Intermediate Similarity NPC475807
0.7222 Intermediate Similarity NPC317242
0.7206 Intermediate Similarity NPC63190
0.72 Intermediate Similarity NPC117137
0.72 Intermediate Similarity NPC66766
0.7188 Intermediate Similarity NPC310228
0.7188 Intermediate Similarity NPC52431
0.7183 Intermediate Similarity NPC470660
0.7183 Intermediate Similarity NPC470659
0.7183 Intermediate Similarity NPC470610
0.7164 Intermediate Similarity NPC472946
0.7162 Intermediate Similarity NPC18857
0.7162 Intermediate Similarity NPC67657
0.7143 Intermediate Similarity NPC471781
0.7123 Intermediate Similarity NPC163597
0.7105 Intermediate Similarity NPC473257
0.7067 Intermediate Similarity NPC287452
0.7027 Intermediate Similarity NPC128951
0.7027 Intermediate Similarity NPC105208
0.7027 Intermediate Similarity NPC477227
0.7027 Intermediate Similarity NPC188793
0.7027 Intermediate Similarity NPC302578
0.7027 Intermediate Similarity NPC192046
0.7 Intermediate Similarity NPC477820
0.697 Remote Similarity NPC95804
0.697 Remote Similarity NPC185547
0.6923 Remote Similarity NPC99480
0.6923 Remote Similarity NPC2572
0.6923 Remote Similarity NPC184049
0.6923 Remote Similarity NPC29342
0.6912 Remote Similarity NPC300442
0.6901 Remote Similarity NPC232925
0.6901 Remote Similarity NPC63588
0.6901 Remote Similarity NPC251201
0.6901 Remote Similarity NPC254845
0.6892 Remote Similarity NPC279575
0.6875 Remote Similarity NPC145245
0.6849 Remote Similarity NPC475458
0.6849 Remote Similarity NPC10476
0.6849 Remote Similarity NPC192501
0.6849 Remote Similarity NPC228994
0.6849 Remote Similarity NPC304499
0.6842 Remote Similarity NPC269333
0.6842 Remote Similarity NPC170595
0.6835 Remote Similarity NPC242016
0.6812 Remote Similarity NPC469328
0.68 Remote Similarity NPC83108
0.68 Remote Similarity NPC214030
0.6795 Remote Similarity NPC212340
0.6774 Remote Similarity NPC161473
0.6769 Remote Similarity NPC475515
0.6769 Remote Similarity NPC215671
0.6769 Remote Similarity NPC87296
0.6765 Remote Similarity NPC219940
0.6765 Remote Similarity NPC159654
0.6765 Remote Similarity NPC167995
0.6765 Remote Similarity NPC281540
0.6765 Remote Similarity NPC118937
0.6761 Remote Similarity NPC241085
0.6761 Remote Similarity NPC66407
0.6761 Remote Similarity NPC129829
0.6761 Remote Similarity NPC299948
0.6761 Remote Similarity NPC254037
0.6761 Remote Similarity NPC470830
0.6761 Remote Similarity NPC107919
0.6757 Remote Similarity NPC158208
0.6757 Remote Similarity NPC91387
0.6757 Remote Similarity NPC231680
0.6757 Remote Similarity NPC270306
0.6757 Remote Similarity NPC196136
0.6757 Remote Similarity NPC243027
0.6719 Remote Similarity NPC3025
0.6712 Remote Similarity NPC248427
0.6709 Remote Similarity NPC471340
0.6709 Remote Similarity NPC260852
0.6709 Remote Similarity NPC69953
0.6709 Remote Similarity NPC478054
0.6707 Remote Similarity NPC22376
0.6667 Remote Similarity NPC133873
0.6667 Remote Similarity NPC470145
0.6667 Remote Similarity NPC192192
0.6667 Remote Similarity NPC231945
0.6667 Remote Similarity NPC477009
0.6667 Remote Similarity NPC216941
0.6667 Remote Similarity NPC238352
0.6622 Remote Similarity NPC472854
0.6622 Remote Similarity NPC471659
0.6618 Remote Similarity NPC114891
0.6615 Remote Similarity NPC322148
0.6582 Remote Similarity NPC475388
0.6582 Remote Similarity NPC475849
0.6582 Remote Similarity NPC472465
0.6579 Remote Similarity NPC474574
0.6579 Remote Similarity NPC133596
0.6579 Remote Similarity NPC11907
0.6579 Remote Similarity NPC64081
0.6579 Remote Similarity NPC476233
0.6575 Remote Similarity NPC1340
0.6575 Remote Similarity NPC470071
0.6575 Remote Similarity NPC187471
0.6575 Remote Similarity NPC157777
0.6575 Remote Similarity NPC127094
0.6575 Remote Similarity NPC131506
0.6575 Remote Similarity NPC252182
0.6571 Remote Similarity NPC44122
0.6562 Remote Similarity NPC471269
0.6538 Remote Similarity NPC470609
0.6533 Remote Similarity NPC24014
0.6533 Remote Similarity NPC27349
0.6528 Remote Similarity NPC99264
0.6522 Remote Similarity NPC476702
0.6515 Remote Similarity NPC476735
0.65 Remote Similarity NPC474266
0.6494 Remote Similarity NPC471045
0.6494 Remote Similarity NPC147993
0.6486 Remote Similarity NPC472341
0.6486 Remote Similarity NPC476422
0.6486 Remote Similarity NPC310608
0.6486 Remote Similarity NPC473238
0.6479 Remote Similarity NPC136813
0.6479 Remote Similarity NPC48079
0.6471 Remote Similarity NPC63111
0.6471 Remote Similarity NPC218585
0.6471 Remote Similarity NPC172622
0.6471 Remote Similarity NPC148174
0.6471 Remote Similarity NPC71460
0.6463 Remote Similarity NPC64862
0.6456 Remote Similarity NPC471661
0.6447 Remote Similarity NPC477601
0.6447 Remote Similarity NPC477602
0.6447 Remote Similarity NPC471658
0.6447 Remote Similarity NPC473916
0.6441 Remote Similarity NPC108441
0.6441 Remote Similarity NPC77550
0.6438 Remote Similarity NPC470041
0.6429 Remote Similarity NPC205618
0.6429 Remote Similarity NPC261782
0.6429 Remote Similarity NPC469326
0.642 Remote Similarity NPC474156
0.642 Remote Similarity NPC291310
0.6418 Remote Similarity NPC9880
0.6418 Remote Similarity NPC87828
0.6418 Remote Similarity NPC230070
0.641 Remote Similarity NPC81074
0.641 Remote Similarity NPC477282
0.6406 Remote Similarity NPC32222
0.6406 Remote Similarity NPC202146
0.64 Remote Similarity NPC477508
0.64 Remote Similarity NPC472945
0.64 Remote Similarity NPC472944
0.64 Remote Similarity NPC470630
0.6393 Remote Similarity NPC294858
0.6389 Remote Similarity NPC167527
0.6389 Remote Similarity NPC319007
0.6389 Remote Similarity NPC472741
0.6379 Remote Similarity NPC144891
0.6364 Remote Similarity NPC180199
0.6364 Remote Similarity NPC171658
0.6364 Remote Similarity NPC477919
0.6351 Remote Similarity NPC471662
0.6351 Remote Similarity NPC127283
0.6351 Remote Similarity NPC8004
0.6341 Remote Similarity NPC266651
0.6338 Remote Similarity NPC142712
0.6333 Remote Similarity NPC84030
0.6333 Remote Similarity NPC287550
0.6333 Remote Similarity NPC223468
0.6333 Remote Similarity NPC147343
0.6333 Remote Similarity NPC198540
0.6333 Remote Similarity NPC176309
0.6329 Remote Similarity NPC16449

  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 NPC475968 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
0.6761 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6667 Remote Similarity NPD4787 Phase 1
0.6441 Remote Similarity NPD386 Approved
0.6441 Remote Similarity NPD388 Approved
0.6418 Remote Similarity NPD3198 Approved
0.6333 Remote Similarity NPD384 Approved
0.6333 Remote Similarity NPD385 Approved
0.6301 Remote Similarity NPD3698 Phase 2
0.6286 Remote Similarity NPD371 Approved
0.6234 Remote Similarity NPD6933 Approved
0.6216 Remote Similarity NPD4244 Approved
0.6216 Remote Similarity NPD4245 Approved
0.6197 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6125 Remote Similarity NPD6928 Phase 2
0.5974 Remote Similarity NPD6926 Approved
0.5974 Remote Similarity NPD6924 Approved
0.5926 Remote Similarity NPD6931 Approved
0.5926 Remote Similarity NPD4748 Discontinued
0.5926 Remote Similarity NPD6930 Phase 2
0.5921 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5921 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5897 Remote Similarity NPD3702 Approved
0.5897 Remote Similarity NPD3703 Phase 2
0.5875 Remote Similarity NPD6118 Approved
0.5875 Remote Similarity NPD6115 Approved
0.5875 Remote Similarity NPD6697 Approved
0.5875 Remote Similarity NPD6114 Approved
0.5867 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5867 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5823 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5814 Remote Similarity NPD7524 Approved
0.5814 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5802 Remote Similarity NPD6929 Approved
0.5789 Remote Similarity NPD4789 Approved
0.5769 Remote Similarity NPD6113 Clinical (unspecified phase)
0.575 Remote Similarity NPD6932 Approved
0.5733 Remote Similarity NPD6705 Phase 1
0.5714 Remote Similarity NPD6695 Phase 3
0.5667 Remote Similarity NPD1462 Approved
0.5667 Remote Similarity NPD8171 Discontinued
0.5647 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6117 Approved
0.5616 Remote Similarity NPD7909 Approved
0.561 Remote Similarity NPD6683 Phase 2

  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