Structure

Physi-Chem Properties

Molecular Weight:  90.07
Volume:  95.321
LogP:  -0.721
LogD:  -1.399
LogS:  0.82
# Rotatable Bonds:  2
TPSA:  40.46
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.491
Synthetic Accessibility Score:  2.931
Fsp3:  1.0
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:  -4.531
MDCK Permeability:  0.0030440939590334892
Pgp-inhibitor:  0.0
Pgp-substrate:  0.019
Human Intestinal Absorption (HIA):  0.027
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.129

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.242
Plasma Protein Binding (PPB):  6.990902900695801%
Volume Distribution (VD):  1.098
Pgp-substrate:  88.76535034179688%

ADMET: Metabolism

CYP1A2-inhibitor:  0.032
CYP1A2-substrate:  0.419
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.619
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.511
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.174
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.174

ADMET: Excretion

Clearance (CL):  6.074
Half-life (T1/2):  0.821

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.082
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.039
Skin Sensitization:  0.188
Carcinogencity:  0.041
Eye Corrosion:  0.879
Eye Irritation:  0.995
Respiratory Toxicity:  0.033

Download Data

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

  Natural Product: NPC88887

Natural Product ID:  NPC88887
Common Name*:   Butane-1,3-Diol
IUPAC Name:   butane-1,3-diol
Synonyms:  
Standard InCHIKey:  PUPZLCDOIYMWBV-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H10O2/c1-4(6)2-3-5/h4-6H,2-3H2,1H3
SMILES:  CC(CCO)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3186475
PubChem CID:   7896
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary 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
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota Flowers Tantempango, Hidalgo, Mexico 2019-May DOI[10.1007/s11130-020-00822-2]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. leaf n.a. DOI[10.1016/S0031-9422(00)94055-X]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. flower n.a. DOI[10.3390/70200245]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[16297615]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. whole plant n.a. PMID[18543151]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[24358188]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24617303]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[26521454]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. PMID[8778246]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31073 Ligusticum chuanxiong Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31073 Ligusticum chuanxiong Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22033 Cnidium officinale Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2837 Aloe spicata Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2997 Aloe africana Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18951 Ligusticum sinense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11578 Aloe vera Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28295 Foeniculum vulgare Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14763 Aloe ferox Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2997 Aloe africana Species Xanthorrhoeaceae 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 30637.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 49052 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 350.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 2.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 76958.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 6916.7 nM PubChem BioAssay data set

☑ 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 NPC88887 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
0.875 High Similarity NPC245688
0.8696 High Similarity NPC299484
0.8462 Intermediate Similarity NPC320326
0.84 Intermediate Similarity NPC140389
0.84 Intermediate Similarity NPC232554
0.8333 Intermediate Similarity NPC39977
0.8261 Intermediate Similarity NPC294703
0.8148 Intermediate Similarity NPC301586
0.8148 Intermediate Similarity NPC33415
0.8077 Intermediate Similarity NPC560
0.8 Intermediate Similarity NPC157340
0.8 Intermediate Similarity NPC87529
0.8 Intermediate Similarity NPC94144
0.8 Intermediate Similarity NPC114270
0.7917 Intermediate Similarity NPC219266
0.7826 Intermediate Similarity NPC236761
0.7826 Intermediate Similarity NPC163707
0.7692 Intermediate Similarity NPC190797
0.76 Intermediate Similarity NPC52403
0.75 Intermediate Similarity NPC159845
0.7407 Intermediate Similarity NPC252154
0.7391 Intermediate Similarity NPC311000
0.7333 Intermediate Similarity NPC127074
0.7333 Intermediate Similarity NPC197207
0.7333 Intermediate Similarity NPC149070
0.7333 Intermediate Similarity NPC187058
0.7333 Intermediate Similarity NPC182541
0.7308 Intermediate Similarity NPC23071
0.7308 Intermediate Similarity NPC256186
0.7308 Intermediate Similarity NPC199270
0.7241 Intermediate Similarity NPC270334
0.7241 Intermediate Similarity NPC110884
0.72 Intermediate Similarity NPC88839
0.72 Intermediate Similarity NPC110344
0.7188 Intermediate Similarity NPC168052
0.7188 Intermediate Similarity NPC191084
0.7188 Intermediate Similarity NPC250870
0.7143 Intermediate Similarity NPC272307
0.7037 Intermediate Similarity NPC213764
0.7037 Intermediate Similarity NPC275462
0.6897 Remote Similarity NPC52362
0.6897 Remote Similarity NPC325345
0.6786 Remote Similarity NPC128335
0.6774 Remote Similarity NPC122962
0.6765 Remote Similarity NPC174396
0.6667 Remote Similarity NPC293908
0.6667 Remote Similarity NPC325034
0.6667 Remote Similarity NPC86412
0.6667 Remote Similarity NPC192065
0.6667 Remote Similarity NPC66052
0.6562 Remote Similarity NPC319034
0.6562 Remote Similarity NPC72324
0.6562 Remote Similarity NPC1748
0.6562 Remote Similarity NPC193062
0.6562 Remote Similarity NPC66124
0.6552 Remote Similarity NPC276332
0.6552 Remote Similarity NPC39869
0.6471 Remote Similarity NPC313405
0.6471 Remote Similarity NPC474914
0.6471 Remote Similarity NPC474392
0.6471 Remote Similarity NPC5505
0.6429 Remote Similarity NPC304786
0.6429 Remote Similarity NPC82694
0.6364 Remote Similarity NPC227267
0.6333 Remote Similarity NPC238135
0.6333 Remote Similarity NPC279895
0.625 Remote Similarity NPC266566
0.625 Remote Similarity NPC317060
0.625 Remote Similarity NPC267243
0.625 Remote Similarity NPC31433
0.625 Remote Similarity NPC321170
0.6176 Remote Similarity NPC97967
0.6154 Remote Similarity NPC106054
0.6087 Remote Similarity NPC2724
0.6071 Remote Similarity NPC318912
0.6071 Remote Similarity NPC237965
0.6 Remote Similarity NPC79544
0.6 Remote Similarity NPC152773
0.6 Remote Similarity NPC324353
0.5946 Remote Similarity NPC222792
0.5946 Remote Similarity NPC316217
0.5946 Remote Similarity NPC306850
0.5938 Remote Similarity NPC225783
0.5938 Remote Similarity NPC147096
0.5938 Remote Similarity NPC24506
0.5938 Remote Similarity NPC28077
0.5938 Remote Similarity NPC185041
0.5938 Remote Similarity NPC236797
0.5938 Remote Similarity NPC112242
0.5938 Remote Similarity NPC198126
0.5938 Remote Similarity NPC163556
0.5882 Remote Similarity NPC81989
0.5862 Remote Similarity NPC272690
0.5862 Remote Similarity NPC35155
0.5806 Remote Similarity NPC261397
0.5789 Remote Similarity NPC99573
0.5789 Remote Similarity NPC111882
0.5789 Remote Similarity NPC227707
0.5789 Remote Similarity NPC320331
0.5789 Remote Similarity NPC266553
0.5789 Remote Similarity NPC102981
0.5789 Remote Similarity NPC88278
0.5758 Remote Similarity NPC307739
0.5758 Remote Similarity NPC313303
0.5758 Remote Similarity NPC76217
0.5758 Remote Similarity NPC126915
0.5714 Remote Similarity NPC325165
0.5714 Remote Similarity NPC316685
0.5667 Remote Similarity NPC317724
0.5667 Remote Similarity NPC127134
0.5667 Remote Similarity NPC149209
0.5641 Remote Similarity NPC474361
0.5641 Remote Similarity NPC35661
0.5625 Remote Similarity NPC327718
0.561 Remote Similarity NPC107091
0.561 Remote Similarity NPC62014
0.561 Remote Similarity NPC207656
0.56 Remote Similarity NPC149567

  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 NPC88887 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
0.8148 Intermediate Similarity NPD8549 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD8226 Approved
0.8 Intermediate Similarity NPD8225 Phase 3
0.7826 Intermediate Similarity NPD8224 Approved
0.7391 Intermediate Similarity NPD8223 Approved
0.7333 Intermediate Similarity NPD8814 Phase 3
0.6897 Remote Similarity NPD8988 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9052 Approved
0.6667 Remote Similarity NPD9051 Approved
0.6667 Remote Similarity NPD9053 Approved
0.6429 Remote Similarity NPD8207 Approved
0.6389 Remote Similarity NPD9056 Approved
0.6389 Remote Similarity NPD9055 Approved
0.625 Remote Similarity NPD8237 Approved
0.6111 Remote Similarity NPD8976 Approved
0.6111 Remote Similarity NPD8977 Phase 3
0.5938 Remote Similarity NPD8618 Approved
0.5938 Remote Similarity NPD8234 Approved
0.5938 Remote Similarity NPD8235 Approved
0.5938 Remote Similarity NPD8236 Phase 1
0.5926 Remote Similarity NPD8196 Approved
0.5789 Remote Similarity NPD8995 Clinical (unspecified phase)
0.5789 Remote Similarity NPD8996 Phase 3
0.5758 Remote Similarity NPD8205 Approved
0.5758 Remote Similarity NPD8558 Approved
0.5758 Remote Similarity NPD8202 Approved
0.5758 Remote Similarity NPD8557 Approved
0.5667 Remote Similarity NPD8989 Approved
0.5667 Remote Similarity NPD8548 Clinical (unspecified phase)
0.5641 Remote Similarity NPD8967 Approved
0.5625 Remote Similarity NPD8619 Approved
0.5625 Remote Similarity NPD8617 Approved
0.561 Remote Similarity NPD9219 Approved
0.561 Remote Similarity NPD9218 Clinical (unspecified phase)
0.56 Remote Similarity NPD7374 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