Structure

Physi-Chem Properties

Molecular Weight:  228.1
Volume:  226.298
LogP:  -0.146
LogD:  -0.291
LogS:  -0.157
# Rotatable Bonds:  5
TPSA:  90.9
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.678
Synthetic Accessibility Score:  3.986
Fsp3:  0.545
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:  -5.025
MDCK Permeability:  0.00011236801947234198
Pgp-inhibitor:  0.0
Pgp-substrate:  0.769
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.055
30% Bioavailability (F30%):  0.022

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.095
Plasma Protein Binding (PPB):  58.593894958496094%
Volume Distribution (VD):  2.373
Pgp-substrate:  42.43535232543945%

ADMET: Metabolism

CYP1A2-inhibitor:  0.044
CYP1A2-substrate:  0.277
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.231
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.894
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.547
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.2

ADMET: Excretion

Clearance (CL):  9.505
Half-life (T1/2):  0.899

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.492
Drug-inuced Liver Injury (DILI):  0.207
AMES Toxicity:  0.015
Rat Oral Acute Toxicity:  0.202
Maximum Recommended Daily Dose:  0.397
Skin Sensitization:  0.3
Carcinogencity:  0.663
Eye Corrosion:  0.003
Eye Irritation:  0.026
Respiratory Toxicity:  0.021

Download Data

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

  Natural Product: NPC478191

Natural Product ID:  NPC478191
Common Name*:   (5Z)-5-[(2R,3R)-2,3-dihydroxybutylidene]-3-[(2R)-2-hydroxypropyl]furan-2-one
IUPAC Name:   (5Z)-5-[(2R,3R)-2,3-dihydroxybutylidene]-3-[(2R)-2-hydroxypropyl]furan-2-one
Synonyms:  
Standard InCHIKey:  BMCSEOVSJWNEJA-VNVWBWAJSA-N
Standard InCHI:  InChI=1S/C11H16O5/c1-6(12)3-8-4-9(16-11(8)15)5-10(14)7(2)13/h4-7,10,12-14H,3H2,1-2H3/b9-5-/t6-,7-,10-/m1/s1
SMILES:  C[C@H](CC1=C/C(=C/[C@H]([C@@H](C)O)O)/OC1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   163017781
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO33695 Plectania sp. Species Sarcosomataceae Eukaryota fruiting body Tibet Plateau Region n.a. DOI[10.1002/ejoc.201600562]

☑ 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

☑ 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 NPC478191 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
1.0 High Similarity NPC478195
1.0 High Similarity NPC478194
1.0 High Similarity NPC478193
1.0 High Similarity NPC478196
1.0 High Similarity NPC478192
0.8611 High Similarity NPC202011
0.8429 Intermediate Similarity NPC470123
0.84 Intermediate Similarity NPC161038
0.8333 Intermediate Similarity NPC287705
0.8289 Intermediate Similarity NPC470705
0.8267 Intermediate Similarity NPC476590
0.8267 Intermediate Similarity NPC114727
0.8219 Intermediate Similarity NPC475982
0.8182 Intermediate Similarity NPC275530
0.8143 Intermediate Similarity NPC473737
0.8143 Intermediate Similarity NPC68110
0.7917 Intermediate Similarity NPC282760
0.7917 Intermediate Similarity NPC19769
0.7901 Intermediate Similarity NPC475046
0.7901 Intermediate Similarity NPC310450
0.7901 Intermediate Similarity NPC474959
0.7901 Intermediate Similarity NPC11383
0.7895 Intermediate Similarity NPC284006
0.7887 Intermediate Similarity NPC2328
0.7857 Intermediate Similarity NPC98519
0.7857 Intermediate Similarity NPC130953
0.7848 Intermediate Similarity NPC28049
0.7838 Intermediate Similarity NPC238223
0.7838 Intermediate Similarity NPC63873
0.7838 Intermediate Similarity NPC474823
0.7821 Intermediate Similarity NPC301207
0.7821 Intermediate Similarity NPC68819
0.7808 Intermediate Similarity NPC248125
0.7808 Intermediate Similarity NPC276299
0.7805 Intermediate Similarity NPC284472
0.7805 Intermediate Similarity NPC229799
0.7805 Intermediate Similarity NPC286770
0.7792 Intermediate Similarity NPC315843
0.775 Intermediate Similarity NPC99651
0.7746 Intermediate Similarity NPC151648
0.7733 Intermediate Similarity NPC475004
0.7722 Intermediate Similarity NPC474818
0.7722 Intermediate Similarity NPC176329
0.7722 Intermediate Similarity NPC49302
0.7722 Intermediate Similarity NPC125365
0.7722 Intermediate Similarity NPC51809
0.7703 Intermediate Similarity NPC132286
0.7701 Intermediate Similarity NPC114345
0.7701 Intermediate Similarity NPC303230
0.7701 Intermediate Similarity NPC6099
0.7671 Intermediate Similarity NPC273600
0.7671 Intermediate Similarity NPC478099
0.7671 Intermediate Similarity NPC478098
0.7639 Intermediate Similarity NPC475073
0.7632 Intermediate Similarity NPC59558
0.7625 Intermediate Similarity NPC221095
0.7625 Intermediate Similarity NPC279214
0.7625 Intermediate Similarity NPC473471
0.7619 Intermediate Similarity NPC473651
0.7619 Intermediate Similarity NPC473669
0.7619 Intermediate Similarity NPC473478
0.7619 Intermediate Similarity NPC110710
0.7619 Intermediate Similarity NPC1083
0.7619 Intermediate Similarity NPC231009
0.7619 Intermediate Similarity NPC182383
0.7619 Intermediate Similarity NPC283085
0.7619 Intermediate Similarity NPC223871
0.7619 Intermediate Similarity NPC286338
0.7619 Intermediate Similarity NPC132496
0.7619 Intermediate Similarity NPC82795
0.7619 Intermediate Similarity NPC474424
0.7619 Intermediate Similarity NPC66346
0.7619 Intermediate Similarity NPC103284
0.7619 Intermediate Similarity NPC107986
0.7595 Intermediate Similarity NPC127118
0.7595 Intermediate Similarity NPC209113
0.7571 Intermediate Similarity NPC189700
0.7568 Intermediate Similarity NPC146811
0.7568 Intermediate Similarity NPC37382
0.7568 Intermediate Similarity NPC201356
0.7564 Intermediate Similarity NPC107654
0.7564 Intermediate Similarity NPC470686
0.7561 Intermediate Similarity NPC150502
0.7532 Intermediate Similarity NPC316185
0.7529 Intermediate Similarity NPC114694
0.7529 Intermediate Similarity NPC473687
0.7529 Intermediate Similarity NPC142117
0.7529 Intermediate Similarity NPC475581
0.7529 Intermediate Similarity NPC279267
0.7529 Intermediate Similarity NPC308412
0.7529 Intermediate Similarity NPC240695
0.7529 Intermediate Similarity NPC69082
0.7529 Intermediate Similarity NPC112685
0.7529 Intermediate Similarity NPC103523
0.7529 Intermediate Similarity NPC210218
0.7529 Intermediate Similarity NPC204686
0.7529 Intermediate Similarity NPC107717
0.7529 Intermediate Similarity NPC232555
0.7529 Intermediate Similarity NPC134865
0.7529 Intermediate Similarity NPC231096
0.7529 Intermediate Similarity NPC134885
0.7529 Intermediate Similarity NPC134807
0.7529 Intermediate Similarity NPC62118
0.7529 Intermediate Similarity NPC219498
0.7529 Intermediate Similarity NPC47937
0.7529 Intermediate Similarity NPC171174
0.75 Intermediate Similarity NPC88877
0.75 Intermediate Similarity NPC476591
0.75 Intermediate Similarity NPC327760
0.75 Intermediate Similarity NPC26810
0.7471 Intermediate Similarity NPC139418
0.7468 Intermediate Similarity NPC260396
0.7467 Intermediate Similarity NPC478097
0.7467 Intermediate Similarity NPC203335
0.7467 Intermediate Similarity NPC122627
0.7442 Intermediate Similarity NPC178215
0.7442 Intermediate Similarity NPC45409
0.7439 Intermediate Similarity NPC162741
0.7439 Intermediate Similarity NPC91332
0.7432 Intermediate Similarity NPC471556
0.7432 Intermediate Similarity NPC471566
0.7432 Intermediate Similarity NPC471565
0.7432 Intermediate Similarity NPC96414
0.7429 Intermediate Similarity NPC135863
0.7407 Intermediate Similarity NPC108816
0.7407 Intermediate Similarity NPC182292
0.7407 Intermediate Similarity NPC93763
0.7386 Intermediate Similarity NPC473904
0.7381 Intermediate Similarity NPC116543
0.7381 Intermediate Similarity NPC40746
0.7381 Intermediate Similarity NPC169575
0.7356 Intermediate Similarity NPC261952
0.7356 Intermediate Similarity NPC81045
0.7356 Intermediate Similarity NPC320569
0.7356 Intermediate Similarity NPC242364
0.7356 Intermediate Similarity NPC21208
0.7356 Intermediate Similarity NPC191929
0.7356 Intermediate Similarity NPC475739
0.7356 Intermediate Similarity NPC20339
0.7356 Intermediate Similarity NPC274446
0.7356 Intermediate Similarity NPC169511
0.7356 Intermediate Similarity NPC100454
0.7356 Intermediate Similarity NPC40376
0.7356 Intermediate Similarity NPC133730
0.7356 Intermediate Similarity NPC280621
0.7356 Intermediate Similarity NPC233551
0.7356 Intermediate Similarity NPC234077
0.7356 Intermediate Similarity NPC48338
0.7356 Intermediate Similarity NPC151403
0.7356 Intermediate Similarity NPC287164
0.7356 Intermediate Similarity NPC171135
0.7356 Intermediate Similarity NPC39754
0.7356 Intermediate Similarity NPC61257
0.7356 Intermediate Similarity NPC172821
0.7349 Intermediate Similarity NPC24417
0.7333 Intermediate Similarity NPC478101
0.7326 Intermediate Similarity NPC469910
0.7308 Intermediate Similarity NPC293114
0.7294 Intermediate Similarity NPC163093
0.7294 Intermediate Similarity NPC156804
0.7294 Intermediate Similarity NPC475706
0.7284 Intermediate Similarity NPC320630
0.7284 Intermediate Similarity NPC116177
0.7284 Intermediate Similarity NPC475711
0.7284 Intermediate Similarity NPC315394
0.7284 Intermediate Similarity NPC7563
0.7284 Intermediate Similarity NPC68156
0.7273 Intermediate Similarity NPC81778
0.7273 Intermediate Similarity NPC42598
0.7273 Intermediate Similarity NPC477011
0.7273 Intermediate Similarity NPC14901
0.7273 Intermediate Similarity NPC91067
0.7273 Intermediate Similarity NPC318963
0.7273 Intermediate Similarity NPC20621
0.7273 Intermediate Similarity NPC473504
0.7273 Intermediate Similarity NPC130359
0.7273 Intermediate Similarity NPC40066
0.7273 Intermediate Similarity NPC236208
0.7273 Intermediate Similarity NPC93794
0.7262 Intermediate Similarity NPC73310
0.7262 Intermediate Similarity NPC65930
0.7262 Intermediate Similarity NPC475159
0.7262 Intermediate Similarity NPC329829
0.7262 Intermediate Similarity NPC229825
0.7262 Intermediate Similarity NPC145914
0.7262 Intermediate Similarity NPC180363
0.7262 Intermediate Similarity NPC473529
0.7262 Intermediate Similarity NPC473712
0.7262 Intermediate Similarity NPC473780
0.7262 Intermediate Similarity NPC94875
0.7262 Intermediate Similarity NPC131002
0.7262 Intermediate Similarity NPC11332
0.7237 Intermediate Similarity NPC478100
0.7237 Intermediate Similarity NPC194871
0.7229 Intermediate Similarity NPC121374
0.7222 Intermediate Similarity NPC322186
0.7222 Intermediate Similarity NPC282644
0.7222 Intermediate Similarity NPC29798
0.7222 Intermediate Similarity NPC11456
0.7222 Intermediate Similarity NPC133600

  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 NPC478191 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
0.6867 Remote Similarity NPD4756 Discovery
0.6849 Remote Similarity NPD9119 Approved
0.6849 Remote Similarity NPD69 Approved
0.6712 Remote Similarity NPD9118 Approved
0.6667 Remote Similarity NPD4246 Clinical (unspecified phase)
0.663 Remote Similarity NPD7838 Discovery
0.6582 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6495 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6452 Remote Similarity NPD6698 Approved
0.6452 Remote Similarity NPD46 Approved
0.6404 Remote Similarity NPD7154 Phase 3
0.6338 Remote Similarity NPD6927 Phase 3
0.6333 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6327 Remote Similarity NPD4225 Approved
0.6292 Remote Similarity NPD5209 Approved
0.6277 Remote Similarity NPD5785 Approved
0.625 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6222 Remote Similarity NPD6110 Phase 1
0.6211 Remote Similarity NPD7983 Approved
0.6196 Remote Similarity NPD4249 Approved
0.6186 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6184 Remote Similarity NPD585 Clinical (unspecified phase)
0.6184 Remote Similarity NPD6109 Phase 1
0.6129 Remote Similarity NPD4250 Approved
0.6129 Remote Similarity NPD4251 Approved
0.6087 Remote Similarity NPD6082 Clinical (unspecified phase)
0.6087 Remote Similarity NPD5363 Approved
0.6056 Remote Similarity NPD4220 Pre-registration
0.6038 Remote Similarity NPD6371 Approved
0.6023 Remote Similarity NPD4271 Approved
0.6023 Remote Similarity NPD4268 Approved
0.5926 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5905 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5889 Remote Similarity NPD4822 Approved
0.5889 Remote Similarity NPD4819 Approved
0.5889 Remote Similarity NPD4820 Approved
0.5889 Remote Similarity NPD4821 Approved
0.5889 Remote Similarity NPD4252 Approved
0.587 Remote Similarity NPD5362 Discontinued
0.5849 Remote Similarity NPD6686 Approved
0.5802 Remote Similarity NPD3197 Phase 1
0.5797 Remote Similarity NPD9411 Phase 1
0.5761 Remote Similarity NPD4269 Approved
0.5761 Remote Similarity NPD4270 Approved
0.5761 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5745 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5741 Remote Similarity NPD2067 Discontinued
0.5728 Remote Similarity NPD5344 Discontinued
0.5714 Remote Similarity NPD7637 Suspended
0.5699 Remote Similarity NPD5331 Approved
0.5699 Remote Similarity NPD5332 Approved
0.5694 Remote Similarity NPD5343 Approved
0.5684 Remote Similarity NPD5786 Approved
0.5682 Remote Similarity NPD1452 Discontinued
0.5667 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5663 Remote Similarity NPD3704 Approved
0.5657 Remote Similarity NPD5779 Approved
0.5657 Remote Similarity NPD5778 Approved
0.5652 Remote Similarity NPD4790 Discontinued
0.5641 Remote Similarity NPD8779 Phase 3
0.5634 Remote Similarity NPD4265 Approved
0.5634 Remote Similarity NPD4222 Approved
0.5631 Remote Similarity NPD7639 Approved
0.5631 Remote Similarity NPD6648 Approved
0.5631 Remote Similarity NPD7640 Approved
0.5625 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5619 Remote Similarity NPD6647 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