Structure

Physi-Chem Properties

Molecular Weight:  618.28
Volume:  580.179
LogP:  4.087
LogD:  3.157
LogS:  -3.901
# Rotatable Bonds:  8
TPSA:  117.84
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  4
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.298
Synthetic Accessibility Score:  5.773
Fsp3:  0.933
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.816
MDCK Permeability:  1.2854001397499815e-05
Pgp-inhibitor:  0.993
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.285
30% Bioavailability (F30%):  0.665

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.064
Plasma Protein Binding (PPB):  84.24763488769531%
Volume Distribution (VD):  0.936
Pgp-substrate:  10.456658363342285%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.59
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.863
CYP2C9-inhibitor:  0.084
CYP2C9-substrate:  0.019
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.061
CYP3A4-inhibitor:  0.435
CYP3A4-substrate:  0.883

ADMET: Excretion

Clearance (CL):  5.223
Half-life (T1/2):  0.296

ADMET: Toxicity

hERG Blockers:  0.057
Human Hepatotoxicity (H-HT):  0.789
Drug-inuced Liver Injury (DILI):  0.03
AMES Toxicity:  0.08
Rat Oral Acute Toxicity:  0.689
Maximum Recommended Daily Dose:  0.919
Skin Sensitization:  0.895
Carcinogencity:  0.682
Eye Corrosion:  0.003
Eye Irritation:  0.012
Respiratory Toxicity:  0.944

Download Data

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

  Natural Product: NPC231784

Natural Product ID:  NPC231784
Common Name*:   Thyrsenol A
IUPAC Name:   (2R,5S)-2-[(4aR,6R,8aS)-6-[(2S,5R)-5-bromo-2,6,6-trimethyloxan-2-yl]-8a-methyl-4a,6,7,8-tetrahydro-4H-pyrano[3,2-b]pyran-2-yl]-5-[(2R,5R)-5-(2-hydroxypropan-2-yl)-2-methyloxolan-2-yl]pentane-1,2,5-triol
Synonyms:  
Standard InCHIKey:  BTRUPJNJODXUNZ-JNQDQRPJSA-N
Standard InCHI:  InChI=1S/C30H51BrO8/c1-25(2,34)21-12-15-27(5,37-21)20(33)11-17-30(35,18-32)24-9-8-22-28(6,38-24)16-13-23(36-22)29(7)14-10-19(31)26(3,4)39-29/h9,19-23,32-35H,8,10-18H2,1-7H3/t19-,20+,21-,22-,23-,27-,28+,29+,30-/m1/s1
SMILES:  CC(C)([C@H]1CC[C@](C)([C@H](CC[C@@](CO)(C2=CC[C@@H]3[C@](C)(CC[C@H]([C@]4(C)CC[C@H](C(C)(C)O4)Br)O3)O2)O)O)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL282025
PubChem CID:   10009012
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO3322 Laurencia viridis Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[21616566]

☑ 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
NPT2 Others Unspecified Inhibition = 15.2 % PMID[547505]
NPT2 Others Unspecified Inhibition = 31.8 % PMID[547505]
NPT2 Others Unspecified Inhibition = 89.6 % PMID[547505]
NPT2 Others Unspecified Inhibition = 97.8 % PMID[547505]

☑ 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 NPC231784 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
0.9286 High Similarity NPC247826
0.8046 Intermediate Similarity NPC5361
0.7831 Intermediate Similarity NPC470173
0.7692 Intermediate Similarity NPC470175
0.759 Intermediate Similarity NPC253123
0.7556 Intermediate Similarity NPC477385
0.7556 Intermediate Similarity NPC477390
0.7471 Intermediate Similarity NPC470176
0.7386 Intermediate Similarity NPC476703
0.7303 Intermediate Similarity NPC137345
0.7303 Intermediate Similarity NPC181838
0.7273 Intermediate Similarity NPC470174
0.7234 Intermediate Similarity NPC477389
0.7234 Intermediate Similarity NPC477387
0.7222 Intermediate Similarity NPC476701
0.7191 Intermediate Similarity NPC244002
0.7158 Intermediate Similarity NPC477386
0.7158 Intermediate Similarity NPC477388
0.7128 Intermediate Similarity NPC298595
0.7113 Intermediate Similarity NPC177668
0.7111 Intermediate Similarity NPC477089
0.7108 Intermediate Similarity NPC250836
0.7083 Intermediate Similarity NPC248312
0.7079 Intermediate Similarity NPC256720
0.7079 Intermediate Similarity NPC236228
0.701 Intermediate Similarity NPC133450
0.6977 Remote Similarity NPC16964
0.697 Remote Similarity NPC280390
0.6932 Remote Similarity NPC476709
0.6923 Remote Similarity NPC68119
0.6923 Remote Similarity NPC13823
0.69 Remote Similarity NPC256368
0.6889 Remote Similarity NPC170148
0.6869 Remote Similarity NPC302584
0.6863 Remote Similarity NPC475332
0.6852 Remote Similarity NPC315836
0.6852 Remote Similarity NPC313668
0.6837 Remote Similarity NPC299527
0.6818 Remote Similarity NPC306085
0.6809 Remote Similarity NPC20072
0.6782 Remote Similarity NPC472947
0.6768 Remote Similarity NPC3952
0.6765 Remote Similarity NPC90583
0.6739 Remote Similarity NPC3852
0.6731 Remote Similarity NPC64348
0.6727 Remote Similarity NPC297945
0.6727 Remote Similarity NPC126897
0.6706 Remote Similarity NPC473722
0.6705 Remote Similarity NPC129630
0.6703 Remote Similarity NPC293223
0.6703 Remote Similarity NPC329626
0.6701 Remote Similarity NPC311163
0.6699 Remote Similarity NPC470683
0.6699 Remote Similarity NPC2666
0.6699 Remote Similarity NPC470684
0.6699 Remote Similarity NPC26307
0.6698 Remote Similarity NPC197736
0.6667 Remote Similarity NPC473294
0.6667 Remote Similarity NPC83702
0.6667 Remote Similarity NPC220167
0.6667 Remote Similarity NPC305698
0.6667 Remote Similarity NPC36954
0.6667 Remote Similarity NPC136699
0.6667 Remote Similarity NPC190859
0.6667 Remote Similarity NPC115607
0.6667 Remote Similarity NPC471472
0.6635 Remote Similarity NPC476895
0.6634 Remote Similarity NPC119379
0.6606 Remote Similarity NPC472896
0.6606 Remote Similarity NPC472897
0.6604 Remote Similarity NPC150463
0.6602 Remote Similarity NPC210717
0.6602 Remote Similarity NPC473333
0.6602 Remote Similarity NPC103165
0.66 Remote Similarity NPC197107
0.66 Remote Similarity NPC191323
0.6598 Remote Similarity NPC51267
0.6598 Remote Similarity NPC471494
0.6598 Remote Similarity NPC242233
0.6596 Remote Similarity NPC100697
0.6593 Remote Similarity NPC12696
0.6593 Remote Similarity NPC36479
0.6591 Remote Similarity NPC304690
0.6591 Remote Similarity NPC74722
0.6574 Remote Similarity NPC472900
0.6574 Remote Similarity NPC472898
0.6574 Remote Similarity NPC472899
0.6571 Remote Similarity NPC469942
0.6569 Remote Similarity NPC472198
0.6569 Remote Similarity NPC14322
0.6566 Remote Similarity NPC87189
0.6566 Remote Similarity NPC309656
0.6566 Remote Similarity NPC228415
0.6562 Remote Similarity NPC106912
0.6562 Remote Similarity NPC2379
0.6562 Remote Similarity NPC263087
0.6562 Remote Similarity NPC31019
0.6562 Remote Similarity NPC27314
0.6552 Remote Similarity NPC82337
0.6552 Remote Similarity NPC259299
0.6552 Remote Similarity NPC73603
0.6538 Remote Similarity NPC240372
0.6538 Remote Similarity NPC261807
0.6538 Remote Similarity NPC266842
0.6538 Remote Similarity NPC476893
0.6535 Remote Similarity NPC472197
0.6535 Remote Similarity NPC208839
0.6535 Remote Similarity NPC114389
0.6535 Remote Similarity NPC472199
0.6535 Remote Similarity NPC276298
0.6531 Remote Similarity NPC171484
0.6531 Remote Similarity NPC149018
0.6526 Remote Similarity NPC16090
0.6526 Remote Similarity NPC15978
0.6514 Remote Similarity NPC231340
0.6509 Remote Similarity NPC470434
0.6509 Remote Similarity NPC471401
0.6509 Remote Similarity NPC20673
0.6509 Remote Similarity NPC476896
0.6509 Remote Similarity NPC9878
0.6505 Remote Similarity NPC476894
0.6505 Remote Similarity NPC471492
0.65 Remote Similarity NPC477917
0.65 Remote Similarity NPC97103
0.6495 Remote Similarity NPC166279
0.6495 Remote Similarity NPC115995
0.6489 Remote Similarity NPC180725
0.6489 Remote Similarity NPC291260
0.6486 Remote Similarity NPC141433
0.6484 Remote Similarity NPC471525
0.6481 Remote Similarity NPC75608
0.6481 Remote Similarity NPC469869
0.6481 Remote Similarity NPC470768
0.6476 Remote Similarity NPC274458
0.6476 Remote Similarity NPC308567
0.6476 Remote Similarity NPC187761
0.6476 Remote Similarity NPC261377
0.6476 Remote Similarity NPC475653
0.6476 Remote Similarity NPC83895
0.6476 Remote Similarity NPC255592
0.6476 Remote Similarity NPC312325
0.6471 Remote Similarity NPC476300
0.6471 Remote Similarity NPC238090
0.6471 Remote Similarity NPC91654
0.6471 Remote Similarity NPC67398
0.6471 Remote Similarity NPC471483
0.6471 Remote Similarity NPC109406
0.6471 Remote Similarity NPC472195
0.6471 Remote Similarity NPC474792
0.6471 Remote Similarity NPC475912
0.6471 Remote Similarity NPC472196
0.6471 Remote Similarity NPC137461
0.6465 Remote Similarity NPC476948
0.6455 Remote Similarity NPC473807
0.6455 Remote Similarity NPC235824
0.6455 Remote Similarity NPC50124
0.6452 Remote Similarity NPC40049
0.6449 Remote Similarity NPC201191
0.6442 Remote Similarity NPC288350
0.6442 Remote Similarity NPC72204
0.6442 Remote Similarity NPC173329
0.6442 Remote Similarity NPC156912
0.6442 Remote Similarity NPC476315
0.6442 Remote Similarity NPC288970
0.6442 Remote Similarity NPC472995
0.6436 Remote Similarity NPC477866
0.6436 Remote Similarity NPC471569
0.6436 Remote Similarity NPC477865
0.6436 Remote Similarity NPC478003
0.6436 Remote Similarity NPC474761
0.6436 Remote Similarity NPC476004
0.6436 Remote Similarity NPC159876
0.6436 Remote Similarity NPC478004
0.6436 Remote Similarity NPC158388
0.6429 Remote Similarity NPC471379
0.6429 Remote Similarity NPC196911
0.6429 Remote Similarity NPC290731
0.6422 Remote Similarity NPC470763
0.6422 Remote Similarity NPC470767
0.6422 Remote Similarity NPC315070
0.6421 Remote Similarity NPC133226
0.6421 Remote Similarity NPC470147
0.6415 Remote Similarity NPC272223
0.6415 Remote Similarity NPC469870
0.6415 Remote Similarity NPC244878
0.6415 Remote Similarity NPC469871
0.6415 Remote Similarity NPC471242
0.6408 Remote Similarity NPC72817
0.6408 Remote Similarity NPC159698
0.6408 Remote Similarity NPC477927
0.6404 Remote Similarity NPC239373
0.6404 Remote Similarity NPC329989
0.64 Remote Similarity NPC474668
0.6396 Remote Similarity NPC221110
0.6396 Remote Similarity NPC180459
0.6396 Remote Similarity NPC195116
0.6396 Remote Similarity NPC285253
0.6396 Remote Similarity NPC471400
0.6392 Remote Similarity NPC320548
0.6392 Remote Similarity NPC107498

  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 NPC231784 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
0.6727 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6633 Remote Similarity NPD7524 Approved
0.6495 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6436 Remote Similarity NPD6698 Approved
0.6436 Remote Similarity NPD46 Approved
0.6392 Remote Similarity NPD6695 Phase 3
0.6321 Remote Similarity NPD8029 Clinical (unspecified phase)
0.63 Remote Similarity NPD4250 Approved
0.63 Remote Similarity NPD4251 Approved
0.6275 Remote Similarity NPD7838 Discovery
0.6214 Remote Similarity NPD7983 Approved
0.62 Remote Similarity NPD4249 Approved
0.6139 Remote Similarity NPD7750 Discontinued
0.6083 Remote Similarity NPD8513 Phase 3
0.6082 Remote Similarity NPD6930 Phase 2
0.6082 Remote Similarity NPD6931 Approved
0.6055 Remote Similarity NPD5344 Discontinued
0.6018 Remote Similarity NPD6686 Approved
0.5979 Remote Similarity NPD6929 Approved
0.595 Remote Similarity NPD8516 Approved
0.595 Remote Similarity NPD7503 Approved
0.595 Remote Similarity NPD8515 Approved
0.595 Remote Similarity NPD8517 Approved
0.5943 Remote Similarity NPD5282 Discontinued
0.5918 Remote Similarity NPD7514 Phase 3
0.5918 Remote Similarity NPD7332 Phase 2
0.5905 Remote Similarity NPD7087 Discontinued
0.59 Remote Similarity NPD7154 Phase 3
0.5856 Remote Similarity NPD7632 Discontinued
0.5833 Remote Similarity NPD6933 Approved
0.582 Remote Similarity NPD8033 Approved
0.5812 Remote Similarity NPD6053 Discontinued
0.5789 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5784 Remote Similarity NPD6893 Approved
0.5773 Remote Similarity NPD6925 Approved
0.5773 Remote Similarity NPD5776 Phase 2
0.5758 Remote Similarity NPD4819 Approved
0.5758 Remote Similarity NPD4822 Approved
0.5758 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5758 Remote Similarity NPD4820 Approved
0.5758 Remote Similarity NPD4821 Approved
0.5743 Remote Similarity NPD6110 Phase 1
0.5738 Remote Similarity NPD8294 Approved
0.5738 Remote Similarity NPD8377 Approved
0.5727 Remote Similarity NPD4225 Approved
0.5714 Remote Similarity NPD8074 Phase 3
0.5714 Remote Similarity NPD7145 Approved
0.5702 Remote Similarity NPD7328 Approved
0.5702 Remote Similarity NPD7327 Approved
0.5701 Remote Similarity NPD5779 Approved
0.5701 Remote Similarity NPD5778 Approved
0.57 Remote Similarity NPD6902 Approved
0.57 Remote Similarity NPD6898 Phase 1
0.5691 Remote Similarity NPD8296 Approved
0.5691 Remote Similarity NPD8380 Approved
0.5691 Remote Similarity NPD8378 Approved
0.5691 Remote Similarity NPD8335 Approved
0.5691 Remote Similarity NPD8379 Approved
0.5686 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5676 Remote Similarity NPD6648 Approved
0.5673 Remote Similarity NPD4751 Clinical (unspecified phase)
0.566 Remote Similarity NPD8522 Clinical (unspecified phase)
0.5656 Remote Similarity NPD7516 Approved
0.5652 Remote Similarity NPD6412 Phase 2
0.5641 Remote Similarity NPD6371 Approved
0.5625 Remote Similarity NPD6926 Approved
0.5625 Remote Similarity NPD6924 Approved
0.562 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5618 Remote Similarity NPD368 Approved
0.5612 Remote Similarity NPD6932 Approved
0.5607 Remote Similarity NPD7637 Suspended
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