Structure

Physi-Chem Properties

Molecular Weight:  470.34
Volume:  517.825
LogP:  3.607
LogD:  3.112
LogS:  -4.862
# Rotatable Bonds:  5
TPSA:  71.44
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.516
Synthetic Accessibility Score:  4.795
Fsp3:  0.833
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.098
MDCK Permeability:  1.2244557183294091e-05
Pgp-inhibitor:  0.603
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.021
20% Bioavailability (F20%):  0.064
30% Bioavailability (F30%):  0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.957
Plasma Protein Binding (PPB):  89.9134292602539%
Volume Distribution (VD):  0.777
Pgp-substrate:  3.52897572517395%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.497
CYP2C19-inhibitor:  0.218
CYP2C19-substrate:  0.931
CYP2C9-inhibitor:  0.514
CYP2C9-substrate:  0.227
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.775
CYP3A4-substrate:  0.817

ADMET: Excretion

Clearance (CL):  7.025
Half-life (T1/2):  0.577

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.169
Drug-inuced Liver Injury (DILI):  0.128
AMES Toxicity:  0.014
Rat Oral Acute Toxicity:  0.038
Maximum Recommended Daily Dose:  0.585
Skin Sensitization:  0.072
Carcinogencity:  0.105
Eye Corrosion:  0.004
Eye Irritation:  0.018
Respiratory Toxicity:  0.949

Download Data

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

  Natural Product: NPC469324

Natural Product ID:  NPC469324
Common Name*:   [(1S,4R)-1,4-Dihydroxy-1-Methyl-7-Propan-2-Yl-2,3,3A,5,6,8A-Hexahydroazulen-4-Yl]Methanesulfonic Acid
IUPAC Name:   [(1S,4R)-1,4-dihydroxy-1-methyl-7-propan-2-yl-2,3,3a,5,6,8a-hexahydroazulen-4-yl]methanesulfonic acid
Synonyms:  
Standard InCHIKey:  ATJUNJLOOOPBEA-WUCCLRPBSA-N
Standard InCHI:  InChI=1S/C15H26O5S/c1-10(2)11-4-7-15(17,9-21(18,19)20)12-5-6-14(3,16)13(12)8-11/h8,10,12-13,16-17H,4-7,9H2,1-3H3,(H,18,19,20)/t12?,13?,14-,15-/m0/s1
SMILES:  CC(C)C1=CC2C(CCC2(C)O)C(CC1)(CS(=O)(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL105433
PubChem CID:   44335313
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002874] Guaianes

*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
NPO30648 Alisma orientale Species Alismataceae Eukaryota rhizome n.a. n.a. PMID[10560729]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. rhizome n.a. PMID[17541191]
NPO30648 Alisma orientale Species Alismataceae Eukaryota Rhizome n.a. n.a. PMID[26425784]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. tuber n.a. PMID[26666273]
NPO30648 Alisma orientale Species Alismataceae Eukaryota n.a. n.a. n.a. Database[HerDing]

☑ 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
NPT32 Organism Mus musculus Mus musculus Inhibition = 2.8 % PMID[558959]
NPT32 Organism Mus musculus Mus musculus Inhibition = -2.2 % PMID[558959]
NPT32 Organism Mus musculus Mus musculus Inhibition = 4.9 % PMID[558959]
NPT32 Organism Mus musculus Mus musculus Inhibition = 16.3 % PMID[558959]
NPT32 Organism Mus musculus Mus musculus Inhibition = 21.3 % PMID[558959]
NPT32 Organism Mus musculus Mus musculus IC50 > 100000.0 nM PMID[558959]

☑ 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 NPC469324 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
0.9306 High Similarity NPC469320
0.8333 Intermediate Similarity NPC205618
0.8333 Intermediate Similarity NPC469326
0.8333 Intermediate Similarity NPC261782
0.7917 Intermediate Similarity NPC63111
0.7895 Intermediate Similarity NPC144647
0.7792 Intermediate Similarity NPC471781
0.7639 Intermediate Similarity NPC469321
0.7397 Intermediate Similarity NPC52431
0.7397 Intermediate Similarity NPC310228
0.7361 Intermediate Similarity NPC278550
0.7037 Intermediate Similarity NPC41886
0.6914 Remote Similarity NPC470041
0.6905 Remote Similarity NPC126969
0.6842 Remote Similarity NPC252809
0.679 Remote Similarity NPC474900
0.675 Remote Similarity NPC136813
0.6711 Remote Similarity NPC5698
0.6667 Remote Similarity NPC224532
0.6667 Remote Similarity NPC474480
0.6627 Remote Similarity NPC471660
0.6623 Remote Similarity NPC323153
0.6591 Remote Similarity NPC30675
0.6575 Remote Similarity NPC192962
0.6548 Remote Similarity NPC300940
0.6543 Remote Similarity NPC472253
0.6543 Remote Similarity NPC472255
0.6533 Remote Similarity NPC274396
0.6512 Remote Similarity NPC152017
0.65 Remote Similarity NPC238352
0.65 Remote Similarity NPC477009
0.6494 Remote Similarity NPC99480
0.6494 Remote Similarity NPC184049
0.6471 Remote Similarity NPC471659
0.6463 Remote Similarity NPC167527
0.6456 Remote Similarity NPC133368
0.6456 Remote Similarity NPC211291
0.6444 Remote Similarity NPC472465
0.6444 Remote Similarity NPC133844
0.6444 Remote Similarity NPC1272
0.6444 Remote Similarity NPC470614
0.642 Remote Similarity NPC272125
0.642 Remote Similarity NPC469328
0.6413 Remote Similarity NPC146850
0.6413 Remote Similarity NPC287015
0.641 Remote Similarity NPC135648
0.6395 Remote Similarity NPC77501
0.6395 Remote Similarity NPC85831
0.6395 Remote Similarity NPC215215
0.6395 Remote Similarity NPC265921
0.6374 Remote Similarity NPC471340
0.6364 Remote Similarity NPC475830
0.6333 Remote Similarity NPC471661
0.6329 Remote Similarity NPC274704
0.6322 Remote Similarity NPC124289
0.6322 Remote Similarity NPC25908
0.6322 Remote Similarity NPC142759
0.6322 Remote Similarity NPC471658
0.6322 Remote Similarity NPC115719
0.6322 Remote Similarity NPC473437
0.6322 Remote Similarity NPC141346
0.6304 Remote Similarity NPC124172
0.6296 Remote Similarity NPC471200
0.6292 Remote Similarity NPC66677
0.6292 Remote Similarity NPC471890
0.6292 Remote Similarity NPC84185
0.6279 Remote Similarity NPC309178
0.6277 Remote Similarity NPC191283
0.625 Remote Similarity NPC279200
0.625 Remote Similarity NPC470832
0.625 Remote Similarity NPC471454
0.6235 Remote Similarity NPC469737
0.6222 Remote Similarity NPC26117
0.6207 Remote Similarity NPC319090
0.6207 Remote Similarity NPC23231
0.6207 Remote Similarity NPC60818
0.6207 Remote Similarity NPC113639
0.6207 Remote Similarity NPC328104
0.6196 Remote Similarity NPC110778
0.6186 Remote Similarity NPC94127
0.618 Remote Similarity NPC470944
0.617 Remote Similarity NPC24277
0.617 Remote Similarity NPC152808
0.617 Remote Similarity NPC201273
0.617 Remote Similarity NPC293287
0.6163 Remote Similarity NPC14352
0.6163 Remote Similarity NPC234527
0.6162 Remote Similarity NPC52044
0.6162 Remote Similarity NPC67584
0.6154 Remote Similarity NPC320525
0.6154 Remote Similarity NPC15978
0.6145 Remote Similarity NPC477791
0.6145 Remote Similarity NPC163290
0.6145 Remote Similarity NPC73603
0.6136 Remote Similarity NPC476317
0.6136 Remote Similarity NPC215481
0.6136 Remote Similarity NPC310643
0.6129 Remote Similarity NPC90446
0.6129 Remote Similarity NPC127606
0.6129 Remote Similarity NPC116613
0.6129 Remote Similarity NPC475798
0.6125 Remote Similarity NPC15152
0.6125 Remote Similarity NPC210346
0.6122 Remote Similarity NPC272293
0.6122 Remote Similarity NPC40821
0.6122 Remote Similarity NPC32862
0.6118 Remote Similarity NPC254845
0.6105 Remote Similarity NPC475313
0.6105 Remote Similarity NPC271967
0.61 Remote Similarity NPC213078
0.6098 Remote Similarity NPC187619
0.6098 Remote Similarity NPC61503
0.6092 Remote Similarity NPC470630
0.6092 Remote Similarity NPC329090
0.6092 Remote Similarity NPC27395
0.6082 Remote Similarity NPC37607
0.6082 Remote Similarity NPC301969
0.6067 Remote Similarity NPC186109
0.6064 Remote Similarity NPC471185
0.6061 Remote Similarity NPC473258
0.6049 Remote Similarity NPC473508
0.6047 Remote Similarity NPC471662
0.6044 Remote Similarity NPC471656
0.6044 Remote Similarity NPC186072
0.6044 Remote Similarity NPC324772
0.6044 Remote Similarity NPC164218
0.6042 Remote Similarity NPC470542
0.6042 Remote Similarity NPC2158
0.604 Remote Similarity NPC161493
0.6026 Remote Similarity NPC119425
0.6024 Remote Similarity NPC230107
0.6024 Remote Similarity NPC311736
0.6023 Remote Similarity NPC313185
0.6023 Remote Similarity NPC89374
0.6023 Remote Similarity NPC251435
0.6022 Remote Similarity NPC477818
0.6022 Remote Similarity NPC141941
0.6022 Remote Similarity NPC320548
0.6022 Remote Similarity NPC193870
0.6 Remote Similarity NPC477522
0.6 Remote Similarity NPC477668
0.6 Remote Similarity NPC6605
0.6 Remote Similarity NPC157781
0.6 Remote Similarity NPC74722
0.6 Remote Similarity NPC304690
0.6 Remote Similarity NPC35519
0.6 Remote Similarity NPC179169
0.6 Remote Similarity NPC181255
0.6 Remote Similarity NPC162109
0.6 Remote Similarity NPC306195
0.6 Remote Similarity NPC87604
0.598 Remote Similarity NPC221615
0.5979 Remote Similarity NPC105495
0.5979 Remote Similarity NPC299527
0.5977 Remote Similarity NPC476709
0.5977 Remote Similarity NPC474140
0.5977 Remote Similarity NPC310608
0.5976 Remote Similarity NPC300593
0.5976 Remote Similarity NPC309300
0.5974 Remote Similarity NPC218525
0.5974 Remote Similarity NPC45387
0.5957 Remote Similarity NPC478102
0.5957 Remote Similarity NPC290052
0.5957 Remote Similarity NPC37005
0.5957 Remote Similarity NPC16887
0.5957 Remote Similarity NPC53011
0.5957 Remote Similarity NPC209802
0.5957 Remote Similarity NPC154893
0.5957 Remote Similarity NPC242016
0.5955 Remote Similarity NPC96319
0.5955 Remote Similarity NPC170148
0.5955 Remote Similarity NPC315261
0.5946 Remote Similarity NPC329773
0.5934 Remote Similarity NPC476701
0.5934 Remote Similarity NPC204270
0.593 Remote Similarity NPC133873
0.593 Remote Similarity NPC475728
0.5918 Remote Similarity NPC107189
0.5918 Remote Similarity NPC473956
0.5918 Remote Similarity NPC472466
0.5918 Remote Similarity NPC475751
0.5904 Remote Similarity NPC300442
0.59 Remote Similarity NPC298919
0.59 Remote Similarity NPC127019
0.5895 Remote Similarity NPC474189
0.5895 Remote Similarity NPC474349
0.5895 Remote Similarity NPC476628
0.5889 Remote Similarity NPC476703
0.5889 Remote Similarity NPC198968
0.5889 Remote Similarity NPC155986
0.5889 Remote Similarity NPC318495
0.5889 Remote Similarity NPC476439
0.5882 Remote Similarity NPC477226
0.5876 Remote Similarity NPC475664
0.5876 Remote Similarity NPC58532
0.5876 Remote Similarity NPC472677
0.5876 Remote Similarity NPC474668
0.587 Remote Similarity NPC236237
0.587 Remote Similarity NPC322313
0.587 Remote Similarity NPC102253

  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 NPC469324 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
0.6421 Remote Similarity NPD7136 Phase 2
0.6279 Remote Similarity NPD4784 Approved
0.6279 Remote Similarity NPD4785 Approved
0.6235 Remote Similarity NPD4243 Approved
0.6129 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6092 Remote Similarity NPD6924 Approved
0.6092 Remote Similarity NPD6926 Approved
0.6044 Remote Similarity NPD6931 Approved
0.6044 Remote Similarity NPD6930 Phase 2
0.6023 Remote Similarity NPD4190 Phase 3
0.6023 Remote Similarity NPD5275 Approved
0.6022 Remote Similarity NPD6695 Phase 3
0.5955 Remote Similarity NPD6933 Approved
0.5955 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5938 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5934 Remote Similarity NPD4195 Approved
0.5934 Remote Similarity NPD6929 Approved
0.5889 Remote Similarity NPD6932 Approved
0.587 Remote Similarity NPD7525 Registered
0.587 Remote Similarity NPD4822 Approved
0.587 Remote Similarity NPD4820 Approved
0.587 Remote Similarity NPD4819 Approved
0.587 Remote Similarity NPD4821 Approved
0.5773 Remote Similarity NPD7524 Approved
0.5773 Remote Similarity NPD7750 Discontinued
0.5761 Remote Similarity NPD6683 Phase 2
0.5755 Remote Similarity NPD4754 Approved
0.5745 Remote Similarity NPD4223 Phase 3
0.5745 Remote Similarity NPD4221 Approved
0.5729 Remote Similarity NPD6893 Approved
0.5714 Remote Similarity NPD6925 Approved
0.5714 Remote Similarity NPD5776 Phase 2
0.5699 Remote Similarity NPD7509 Discontinued
0.5699 Remote Similarity NPD7514 Phase 3
0.5684 Remote Similarity NPD5331 Approved
0.5684 Remote Similarity NPD5362 Discontinued
0.5684 Remote Similarity NPD5332 Approved
0.5667 Remote Similarity NPD6942 Approved
0.5667 Remote Similarity NPD7339 Approved
0.5652 Remote Similarity NPD4268 Approved
0.5652 Remote Similarity NPD4271 Approved
0.5652 Remote Similarity NPD7145 Approved
0.5638 Remote Similarity NPD4790 Discontinued
0.5638 Remote Similarity NPD5369 Approved
0.5632 Remote Similarity NPD6922 Approved
0.5632 Remote Similarity NPD6923 Approved
0.5625 Remote Similarity NPD3668 Phase 3
0.5625 Remote Similarity NPD4197 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