Structure

Physi-Chem Properties

Molecular Weight:  170.09
Volume:  170.842
LogP:  0.02
LogD:  0.336
LogS:  -0.545
# Rotatable Bonds:  2
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.57
Synthetic Accessibility Score:  4.301
Fsp3:  0.778
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.775
MDCK Permeability:  0.0006545031792484224
Pgp-inhibitor:  0.0
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.048
20% Bioavailability (F20%):  0.861
30% Bioavailability (F30%):  0.052

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.288
Plasma Protein Binding (PPB):  18.506031036376953%
Volume Distribution (VD):  0.674
Pgp-substrate:  71.7384262084961%

ADMET: Metabolism

CYP1A2-inhibitor:  0.081
CYP1A2-substrate:  0.204
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.51
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.069
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.105
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.233

ADMET: Excretion

Clearance (CL):  3.95
Half-life (T1/2):  0.832

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.336
Drug-inuced Liver Injury (DILI):  0.964
AMES Toxicity:  0.578
Rat Oral Acute Toxicity:  0.609
Maximum Recommended Daily Dose:  0.066
Skin Sensitization:  0.321
Carcinogencity:  0.778
Eye Corrosion:  0.062
Eye Irritation:  0.971
Respiratory Toxicity:  0.134

Download Data

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

  Natural Product: NPC59442

Natural Product ID:  NPC59442
Common Name*:   ((3Ar,4S,6Ar)-3,3A,4,6A-Tetrahydro-2H-Cyclopenta[B]Furan-4,5-Diyl)Dimethanol
IUPAC Name:   [(3aR,4S,6aR)-5-(hydroxymethyl)-3,3a,4,6a-tetrahydro-2H-cyclopenta[b]furan-4-yl]methanol
Synonyms:  
Standard InCHIKey:  QCZMBBWKHAYATJ-HLTSFMKQSA-N
Standard InCHI:  InChI=1S/C9H14O3/c10-4-6-3-9-7(1-2-12-9)8(6)5-11/h3,7-11H,1-2,4-5H2/t7-,8-,9+/m1/s1
SMILES:  C1CO[C@H]2C=C(CO)[C@@H](CO)[C@@H]12
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1172170
PubChem CID:   11084315
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002648] Tetrahydrofurans

*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
NPO12492 Dictyophora indusiata Species Phallaceae Eukaryota n.a. n.a. n.a. PMID[12502311]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2890 Scrophularia lepidota Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3211 Liatris microcephala Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12492 Dictyophora indusiata Species Phallaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1350 Danaus plexippus Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10035 Ficus pantoniana Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2890 Scrophularia lepidota Species Scrophulariaceae 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
NPT1333 Individual Protein Enoyl-acyl-carrier protein reductase Plasmodium falciparum IC50 = 100.0 ug.mL-1 PMID[509155]

☑ 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 NPC59442 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
0.7949 Intermediate Similarity NPC212363
0.7625 Intermediate Similarity NPC470658
0.7403 Intermediate Similarity NPC470944
0.7308 Intermediate Similarity NPC476701
0.7297 Intermediate Similarity NPC477086
0.7297 Intermediate Similarity NPC477087
0.7273 Intermediate Similarity NPC471454
0.7262 Intermediate Similarity NPC104129
0.7262 Intermediate Similarity NPC249408
0.72 Intermediate Similarity NPC477085
0.7143 Intermediate Similarity NPC152017
0.7143 Intermediate Similarity NPC473508
0.7123 Intermediate Similarity NPC305698
0.7101 Intermediate Similarity NPC99487
0.7089 Intermediate Similarity NPC86971
0.7083 Intermediate Similarity NPC311736
0.7073 Intermediate Similarity NPC136699
0.7073 Intermediate Similarity NPC220167
0.7059 Intermediate Similarity NPC226848
0.7059 Intermediate Similarity NPC155025
0.7024 Intermediate Similarity NPC142583
0.7013 Intermediate Similarity NPC265921
0.7013 Intermediate Similarity NPC215215
0.7013 Intermediate Similarity NPC85831
0.6988 Remote Similarity NPC119001
0.6986 Remote Similarity NPC477791
0.6986 Remote Similarity NPC163290
0.6986 Remote Similarity NPC259299
0.6951 Remote Similarity NPC471340
0.6944 Remote Similarity NPC19569
0.6944 Remote Similarity NPC473722
0.6933 Remote Similarity NPC470041
0.6932 Remote Similarity NPC262133
0.6932 Remote Similarity NPC470013
0.6932 Remote Similarity NPC323008
0.6932 Remote Similarity NPC470010
0.6923 Remote Similarity NPC256720
0.6923 Remote Similarity NPC236228
0.6897 Remote Similarity NPC131209
0.6892 Remote Similarity NPC224532
0.6875 Remote Similarity NPC55304
0.6875 Remote Similarity NPC226226
0.6854 Remote Similarity NPC220221
0.6842 Remote Similarity NPC472254
0.6835 Remote Similarity NPC476439
0.6835 Remote Similarity NPC84360
0.6835 Remote Similarity NPC476703
0.6818 Remote Similarity NPC280390
0.68 Remote Similarity NPC74722
0.68 Remote Similarity NPC472947
0.68 Remote Similarity NPC304690
0.6795 Remote Similarity NPC23231
0.6795 Remote Similarity NPC60818
0.6761 Remote Similarity NPC274704
0.6761 Remote Similarity NPC321867
0.6761 Remote Similarity NPC207007
0.6761 Remote Similarity NPC68679
0.6757 Remote Similarity NPC73603
0.675 Remote Similarity NPC477089
0.6747 Remote Similarity NPC188717
0.6747 Remote Similarity NPC211455
0.6747 Remote Similarity NPC477667
0.6744 Remote Similarity NPC91248
0.6742 Remote Similarity NPC198853
0.6742 Remote Similarity NPC477131
0.6714 Remote Similarity NPC122239
0.6714 Remote Similarity NPC475931
0.6711 Remote Similarity NPC129630
0.6711 Remote Similarity NPC254845
0.6711 Remote Similarity NPC4299
0.6709 Remote Similarity NPC170148
0.6707 Remote Similarity NPC52861
0.6707 Remote Similarity NPC471661
0.6705 Remote Similarity NPC133698
0.6667 Remote Similarity NPC167527
0.6667 Remote Similarity NPC279200
0.6667 Remote Similarity NPC304886
0.6667 Remote Similarity NPC190859
0.6667 Remote Similarity NPC52044
0.6667 Remote Similarity NPC474280
0.6628 Remote Similarity NPC316629
0.6625 Remote Similarity NPC7563
0.6625 Remote Similarity NPC116177
0.6625 Remote Similarity NPC320630
0.6622 Remote Similarity NPC272125
0.6622 Remote Similarity NPC162309
0.662 Remote Similarity NPC471081
0.6596 Remote Similarity NPC86077
0.6596 Remote Similarity NPC250545
0.6591 Remote Similarity NPC470817
0.6591 Remote Similarity NPC37607
0.6591 Remote Similarity NPC301969
0.6579 Remote Similarity NPC144647
0.6579 Remote Similarity NPC217570
0.6579 Remote Similarity NPC101622
0.6579 Remote Similarity NPC90115
0.6575 Remote Similarity NPC300593
0.6575 Remote Similarity NPC110241
0.6556 Remote Similarity NPC472467
0.6556 Remote Similarity NPC144202
0.6552 Remote Similarity NPC473715
0.6548 Remote Similarity NPC472473
0.6548 Remote Similarity NPC116543
0.6548 Remote Similarity NPC250315
0.6548 Remote Similarity NPC52923
0.6543 Remote Similarity NPC196653
0.6543 Remote Similarity NPC471465
0.6538 Remote Similarity NPC14352
0.6538 Remote Similarity NPC476709
0.6538 Remote Similarity NPC234527
0.6533 Remote Similarity NPC472255
0.6533 Remote Similarity NPC136813
0.6533 Remote Similarity NPC472253
0.6522 Remote Similarity NPC161493
0.6517 Remote Similarity NPC475925
0.6512 Remote Similarity NPC478112
0.6512 Remote Similarity NPC477668
0.6512 Remote Similarity NPC472379
0.6506 Remote Similarity NPC24417
0.65 Remote Similarity NPC229655
0.65 Remote Similarity NPC68819
0.65 Remote Similarity NPC126969
0.6494 Remote Similarity NPC471781
0.6486 Remote Similarity NPC187619
0.6484 Remote Similarity NPC67584
0.6484 Remote Similarity NPC170120
0.6477 Remote Similarity NPC299527
0.6477 Remote Similarity NPC470819
0.6477 Remote Similarity NPC268298
0.6477 Remote Similarity NPC295312
0.6471 Remote Similarity NPC83702
0.6471 Remote Similarity NPC194859
0.6471 Remote Similarity NPC224386
0.6471 Remote Similarity NPC476804
0.6471 Remote Similarity NPC32676
0.6463 Remote Similarity NPC89128
0.6463 Remote Similarity NPC167881
0.6463 Remote Similarity NPC98557
0.6463 Remote Similarity NPC204270
0.6463 Remote Similarity NPC477088
0.6458 Remote Similarity NPC86095
0.6456 Remote Similarity NPC114727
0.6456 Remote Similarity NPC476590
0.6452 Remote Similarity NPC221615
0.6447 Remote Similarity NPC272961
0.6444 Remote Similarity NPC135776
0.6444 Remote Similarity NPC27531
0.6438 Remote Similarity NPC133368
0.6438 Remote Similarity NPC211291
0.6437 Remote Similarity NPC237540
0.6437 Remote Similarity NPC160138
0.6429 Remote Similarity NPC229825
0.6429 Remote Similarity NPC472465
0.6429 Remote Similarity NPC89555
0.6421 Remote Similarity NPC261117
0.6421 Remote Similarity NPC310804
0.642 Remote Similarity NPC477425
0.642 Remote Similarity NPC474278
0.642 Remote Similarity NPC474826
0.642 Remote Similarity NPC477426
0.642 Remote Similarity NPC477427
0.6418 Remote Similarity NPC35756
0.6413 Remote Similarity NPC213078
0.641 Remote Similarity NPC471662
0.6404 Remote Similarity NPC209816
0.6404 Remote Similarity NPC129419
0.6404 Remote Similarity NPC295668
0.6404 Remote Similarity NPC475855
0.6404 Remote Similarity NPC71533
0.6404 Remote Similarity NPC106510
0.64 Remote Similarity NPC267027
0.64 Remote Similarity NPC326310
0.6395 Remote Similarity NPC21469
0.6392 Remote Similarity NPC243998
0.6392 Remote Similarity NPC166115
0.6389 Remote Similarity NPC66020
0.6386 Remote Similarity NPC76054
0.6383 Remote Similarity NPC22149
0.6383 Remote Similarity NPC255677
0.6383 Remote Similarity NPC306344
0.6377 Remote Similarity NPC232247
0.6377 Remote Similarity NPC251666
0.6375 Remote Similarity NPC313185
0.6364 Remote Similarity NPC471952
0.6364 Remote Similarity NPC16964
0.6364 Remote Similarity NPC475991
0.6364 Remote Similarity NPC329989
0.6364 Remote Similarity NPC239373
0.6353 Remote Similarity NPC473390
0.6353 Remote Similarity NPC231601
0.6353 Remote Similarity NPC40746
0.6353 Remote Similarity NPC169575
0.6353 Remote Similarity NPC131669
0.6351 Remote Similarity NPC309300
0.6341 Remote Similarity NPC93763
0.6341 Remote Similarity NPC108816
0.6341 Remote Similarity NPC137345
0.6341 Remote Similarity NPC267231
0.6341 Remote Similarity NPC181838
0.6341 Remote Similarity NPC4436

  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 NPC59442 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 NPD368 Approved
0.6706 Remote Similarity NPD4249 Approved
0.6628 Remote Similarity NPD4251 Approved
0.6628 Remote Similarity NPD4250 Approved
0.6585 Remote Similarity NPD7332 Phase 2
0.6471 Remote Similarity NPD7338 Clinical (unspecified phase)
0.642 Remote Similarity NPD6925 Approved
0.642 Remote Similarity NPD5776 Phase 2
0.6395 Remote Similarity NPD6082 Clinical (unspecified phase)
0.6386 Remote Similarity NPD7514 Phase 3
0.6353 Remote Similarity NPD6695 Phase 3
0.6353 Remote Similarity NPD5362 Discontinued
0.6341 Remote Similarity NPD7145 Approved
0.6341 Remote Similarity NPD7322 Clinical (unspecified phase)
0.631 Remote Similarity NPD6902 Approved
0.631 Remote Similarity NPD6898 Phase 1
0.6292 Remote Similarity NPD1695 Approved
0.6265 Remote Similarity NPD6929 Approved
0.619 Remote Similarity NPD6931 Approved
0.619 Remote Similarity NPD5790 Clinical (unspecified phase)
0.619 Remote Similarity NPD6930 Phase 2
0.6143 Remote Similarity NPD342 Phase 1
0.6118 Remote Similarity NPD4790 Discontinued
0.6067 Remote Similarity NPD7750 Discontinued
0.6067 Remote Similarity NPD7524 Approved
0.6024 Remote Similarity NPD6932 Approved
0.5978 Remote Similarity NPD7637 Suspended
0.5977 Remote Similarity NPD5331 Approved
0.5977 Remote Similarity NPD5332 Approved
0.5977 Remote Similarity NPD7154 Phase 3
0.5952 Remote Similarity NPD4271 Approved
0.5952 Remote Similarity NPD4268 Approved
0.5949 Remote Similarity NPD6923 Approved
0.5949 Remote Similarity NPD6922 Approved
0.5926 Remote Similarity NPD4732 Discontinued
0.5889 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5882 Remote Similarity NPD6683 Phase 2
0.5875 Remote Similarity NPD7143 Approved
0.5875 Remote Similarity NPD7144 Approved
0.587 Remote Similarity NPD46 Approved
0.587 Remote Similarity NPD7838 Discovery
0.587 Remote Similarity NPD6698 Approved
0.5854 Remote Similarity NPD6926 Approved
0.5854 Remote Similarity NPD6924 Approved
0.5843 Remote Similarity NPD6893 Approved
0.5842 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5814 Remote Similarity NPD4819 Approved
0.5814 Remote Similarity NPD4821 Approved
0.5814 Remote Similarity NPD4820 Approved
0.5814 Remote Similarity NPD7509 Discontinued
0.5814 Remote Similarity NPD4822 Approved
0.5806 Remote Similarity NPD7087 Discontinued
0.5802 Remote Similarity NPD7152 Approved
0.5802 Remote Similarity NPD7151 Approved
0.5802 Remote Similarity NPD7150 Approved
0.5795 Remote Similarity NPD6110 Phase 1
0.5789 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5783 Remote Similarity NPD8264 Approved
0.5765 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5758 Remote Similarity NPD4265 Approved
0.5743 Remote Similarity NPD6640 Phase 3
0.5714 Remote Similarity NPD7639 Approved
0.5714 Remote Similarity NPD6933 Approved
0.5714 Remote Similarity NPD7640 Approved
0.5699 Remote Similarity NPD7136 Phase 2
0.5684 Remote Similarity NPD5282 Discontinued
0.5676 Remote Similarity NPD585 Clinical (unspecified phase)
0.5673 Remote Similarity NPD6371 Approved
0.5657 Remote Similarity NPD5344 Discontinued
0.5641 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5638 Remote Similarity NPD7983 Approved
0.5632 Remote Similarity NPD4252 Approved
0.5612 Remote Similarity NPD7638 Approved
0.5612 Remote Similarity NPD8029 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