Structure

Physi-Chem Properties

Molecular Weight:  228.14
Volume:  237.44
LogP:  1.722
LogD:  2.026
LogS:  -2.584
# Rotatable Bonds:  2
TPSA:  66.76
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.55
Synthetic Accessibility Score:  4.247
Fsp3:  0.75
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:  -4.589
MDCK Permeability:  0.00010093054152093828
Pgp-inhibitor:  0.006
Pgp-substrate:  0.031
Human Intestinal Absorption (HIA):  0.931
20% Bioavailability (F20%):  0.743
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.992
Plasma Protein Binding (PPB):  88.28170013427734%
Volume Distribution (VD):  0.542
Pgp-substrate:  9.091238975524902%

ADMET: Metabolism

CYP1A2-inhibitor:  0.066
CYP1A2-substrate:  0.112
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.398
CYP2C9-inhibitor:  0.02
CYP2C9-substrate:  0.926
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.228
CYP3A4-inhibitor:  0.056
CYP3A4-substrate:  0.138

ADMET: Excretion

Clearance (CL):  5.491
Half-life (T1/2):  0.909

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.354
Drug-inuced Liver Injury (DILI):  0.057
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.166
Maximum Recommended Daily Dose:  0.228
Skin Sensitization:  0.437
Carcinogencity:  0.268
Eye Corrosion:  0.01
Eye Irritation:  0.205
Respiratory Toxicity:  0.116

Download Data

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

  Natural Product: NPC25298

Natural Product ID:  NPC25298
Common Name*:   Herbarumin I
IUPAC Name:   (2R,3S,4S,5E)-3,4-dihydroxy-2-propyl-2,3,4,7,8,9-hexahydrooxecin-10-one
Synonyms:   herbarumin I
Standard InCHIKey:  IZFXFVSOQMEZKB-MNFMDYEBSA-N
Standard InCHI:  InChI=1S/C12H20O4/c1-2-6-10-12(15)9(13)7-4-3-5-8-11(14)16-10/h4,7,9-10,12-13,15H,2-3,5-6,8H2,1H3/b7-4+/t9-,10+,12-/m0/s1
SMILES:  CCC[C@@H]1[C@H]([C@H](/C=C/CCCC(=O)O1)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453686
PubChem CID:   10751829
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001796] Oxocins

*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
NPO2324 Phoma herbarum Species Didymellaceae Eukaryota n.a. n.a. n.a. PMID[12713403]
NPO2324 Phoma herbarum Species Didymellaceae 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
NPT2 Others Unspecified IC50 = 14200.0 nM PMID[568421]

☑ 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 NPC25298 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
0.9688 High Similarity NPC130618
0.9194 High Similarity NPC113293
0.8696 High Similarity NPC470435
0.8438 Intermediate Similarity NPC81896
0.8438 Intermediate Similarity NPC321919
0.8333 Intermediate Similarity NPC475221
0.8261 Intermediate Similarity NPC470436
0.8261 Intermediate Similarity NPC475982
0.8235 Intermediate Similarity NPC26500
0.8235 Intermediate Similarity NPC330426
0.8235 Intermediate Similarity NPC478097
0.8235 Intermediate Similarity NPC127091
0.8235 Intermediate Similarity NPC271921
0.8235 Intermediate Similarity NPC22101
0.8235 Intermediate Similarity NPC104537
0.8235 Intermediate Similarity NPC148192
0.8235 Intermediate Similarity NPC99619
0.8235 Intermediate Similarity NPC478100
0.8209 Intermediate Similarity NPC476657
0.8209 Intermediate Similarity NPC476655
0.8209 Intermediate Similarity NPC478098
0.8209 Intermediate Similarity NPC476654
0.8209 Intermediate Similarity NPC478099
0.8194 Intermediate Similarity NPC473582
0.8116 Intermediate Similarity NPC48218
0.8116 Intermediate Similarity NPC473559
0.8116 Intermediate Similarity NPC141481
0.8116 Intermediate Similarity NPC324981
0.8088 Intermediate Similarity NPC476659
0.8088 Intermediate Similarity NPC476656
0.8088 Intermediate Similarity NPC478101
0.8056 Intermediate Similarity NPC326504
0.8056 Intermediate Similarity NPC473489
0.803 Intermediate Similarity NPC321838
0.7971 Intermediate Similarity NPC473829
0.7971 Intermediate Similarity NPC475443
0.7969 Intermediate Similarity NPC323436
0.7945 Intermediate Similarity NPC473948
0.7941 Intermediate Similarity NPC19769
0.7887 Intermediate Similarity NPC476660
0.7879 Intermediate Similarity NPC327112
0.7867 Intermediate Similarity NPC318481
0.7857 Intermediate Similarity NPC63873
0.7857 Intermediate Similarity NPC209327
0.7857 Intermediate Similarity NPC273508
0.7838 Intermediate Similarity NPC190400
0.7838 Intermediate Similarity NPC49392
0.7826 Intermediate Similarity NPC201356
0.7794 Intermediate Similarity NPC476658
0.7778 Intermediate Similarity NPC137538
0.7763 Intermediate Similarity NPC475210
0.7746 Intermediate Similarity NPC473772
0.7733 Intermediate Similarity NPC474278
0.7727 Intermediate Similarity NPC322186
0.7727 Intermediate Similarity NPC318306
0.7681 Intermediate Similarity NPC96414
0.7671 Intermediate Similarity NPC325627
0.7656 Intermediate Similarity NPC52264
0.7647 Intermediate Similarity NPC29697
0.7639 Intermediate Similarity NPC42526
0.7612 Intermediate Similarity NPC328311
0.7571 Intermediate Similarity NPC83965
0.7571 Intermediate Similarity NPC276299
0.7568 Intermediate Similarity NPC474321
0.7538 Intermediate Similarity NPC327388
0.7536 Intermediate Similarity NPC470808
0.7536 Intermediate Similarity NPC470320
0.75 Intermediate Similarity NPC66460
0.75 Intermediate Similarity NPC320305
0.75 Intermediate Similarity NPC325929
0.75 Intermediate Similarity NPC328776
0.75 Intermediate Similarity NPC201939
0.75 Intermediate Similarity NPC271282
0.7468 Intermediate Similarity NPC474252
0.7467 Intermediate Similarity NPC260396
0.7465 Intermediate Similarity NPC49863
0.7463 Intermediate Similarity NPC97570
0.7463 Intermediate Similarity NPC329249
0.7429 Intermediate Similarity NPC245947
0.7429 Intermediate Similarity NPC136164
0.7429 Intermediate Similarity NPC255863
0.7429 Intermediate Similarity NPC323477
0.7424 Intermediate Similarity NPC323498
0.7424 Intermediate Similarity NPC211752
0.7424 Intermediate Similarity NPC323597
0.7403 Intermediate Similarity NPC248775
0.7397 Intermediate Similarity NPC202011
0.7397 Intermediate Similarity NPC476037
0.7391 Intermediate Similarity NPC54925
0.7368 Intermediate Similarity NPC326661
0.7368 Intermediate Similarity NPC68819
0.7353 Intermediate Similarity NPC243532
0.7342 Intermediate Similarity NPC297440
0.7333 Intermediate Similarity NPC474280
0.7324 Intermediate Similarity NPC328653
0.7324 Intermediate Similarity NPC146811
0.7308 Intermediate Similarity NPC470149
0.7308 Intermediate Similarity NPC1180
0.7308 Intermediate Similarity NPC180725
0.7308 Intermediate Similarity NPC470148
0.7286 Intermediate Similarity NPC328089
0.7286 Intermediate Similarity NPC226592
0.7286 Intermediate Similarity NPC68343
0.7273 Intermediate Similarity NPC474026
0.7273 Intermediate Similarity NPC475711
0.726 Intermediate Similarity NPC143396
0.726 Intermediate Similarity NPC236208
0.725 Intermediate Similarity NPC475046
0.725 Intermediate Similarity NPC11383
0.725 Intermediate Similarity NPC310450
0.725 Intermediate Similarity NPC474959
0.7246 Intermediate Similarity NPC26810
0.7246 Intermediate Similarity NPC477829
0.7237 Intermediate Similarity NPC161038
0.7222 Intermediate Similarity NPC473357
0.7222 Intermediate Similarity NPC193029
0.7222 Intermediate Similarity NPC122627
0.7215 Intermediate Similarity NPC470147
0.7215 Intermediate Similarity NPC133226
0.7206 Intermediate Similarity NPC322002
0.72 Intermediate Similarity NPC284006
0.72 Intermediate Similarity NPC329890
0.7183 Intermediate Similarity NPC273600
0.7183 Intermediate Similarity NPC470123
0.7183 Intermediate Similarity NPC296436
0.7183 Intermediate Similarity NPC318420
0.7183 Intermediate Similarity NPC176215
0.7183 Intermediate Similarity NPC326268
0.7183 Intermediate Similarity NPC317881
0.7183 Intermediate Similarity NPC323045
0.7179 Intermediate Similarity NPC473471
0.7179 Intermediate Similarity NPC127526
0.7179 Intermediate Similarity NPC133377
0.7164 Intermediate Similarity NPC44542
0.7162 Intermediate Similarity NPC473361
0.7162 Intermediate Similarity NPC329904
0.7162 Intermediate Similarity NPC476012
0.716 Intermediate Similarity NPC229799
0.716 Intermediate Similarity NPC284472
0.716 Intermediate Similarity NPC286770
0.7143 Intermediate Similarity NPC127118
0.7143 Intermediate Similarity NPC301207
0.7143 Intermediate Similarity NPC209113
0.7143 Intermediate Similarity NPC470899
0.7125 Intermediate Similarity NPC150502
0.7125 Intermediate Similarity NPC52861
0.7125 Intermediate Similarity NPC24417
0.7123 Intermediate Similarity NPC474823
0.7108 Intermediate Similarity NPC478112
0.7108 Intermediate Similarity NPC278283
0.7108 Intermediate Similarity NPC469910
0.7105 Intermediate Similarity NPC107654
0.7105 Intermediate Similarity NPC315843
0.7105 Intermediate Similarity NPC474545
0.7101 Intermediate Similarity NPC258788
0.7089 Intermediate Similarity NPC99651
0.7089 Intermediate Similarity NPC321728
0.7073 Intermediate Similarity NPC32676
0.7067 Intermediate Similarity NPC319163
0.7067 Intermediate Similarity NPC67076
0.7067 Intermediate Similarity NPC293114
0.7051 Intermediate Similarity NPC474818
0.7051 Intermediate Similarity NPC125365
0.7051 Intermediate Similarity NPC51809
0.7051 Intermediate Similarity NPC110813
0.7051 Intermediate Similarity NPC49302
0.7051 Intermediate Similarity NPC176329
0.7051 Intermediate Similarity NPC275530
0.7037 Intermediate Similarity NPC229825
0.7027 Intermediate Similarity NPC475004
0.7024 Intermediate Similarity NPC45409
0.7015 Intermediate Similarity NPC472808
0.7015 Intermediate Similarity NPC324224
0.7013 Intermediate Similarity NPC478193
0.7013 Intermediate Similarity NPC478195
0.7013 Intermediate Similarity NPC478196
0.7013 Intermediate Similarity NPC478194
0.7013 Intermediate Similarity NPC478191
0.7013 Intermediate Similarity NPC478192
0.7 Intermediate Similarity NPC475984
0.7 Intermediate Similarity NPC55376
0.6988 Remote Similarity NPC21469
0.6984 Remote Similarity NPC163345
0.6977 Remote Similarity NPC474232
0.6977 Remote Similarity NPC313670
0.6974 Remote Similarity NPC329914
0.6974 Remote Similarity NPC185186
0.6974 Remote Similarity NPC327383
0.6962 Remote Similarity NPC279214
0.6962 Remote Similarity NPC27949
0.6962 Remote Similarity NPC471465
0.6962 Remote Similarity NPC260814
0.6962 Remote Similarity NPC317263
0.6962 Remote Similarity NPC218817
0.6962 Remote Similarity NPC196653
0.6962 Remote Similarity NPC182292
0.6962 Remote Similarity NPC221095
0.6962 Remote Similarity NPC39547
0.6962 Remote Similarity NPC323249
0.6962 Remote Similarity NPC11796

  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 NPC25298 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
0.7879 Intermediate Similarity NPD4246 Clinical (unspecified phase)
0.7465 Intermediate Similarity NPD4247 Clinical (unspecified phase)
0.7313 Intermediate Similarity NPD6109 Phase 1
0.7286 Intermediate Similarity NPD3197 Phase 1
0.7215 Intermediate Similarity NPD5790 Clinical (unspecified phase)
0.7059 Intermediate Similarity NPD585 Clinical (unspecified phase)
0.6962 Remote Similarity NPD4268 Approved
0.6962 Remote Similarity NPD4271 Approved
0.6951 Remote Similarity NPD7154 Phase 3
0.6897 Remote Similarity NPD7983 Approved
0.679 Remote Similarity NPD4820 Approved
0.679 Remote Similarity NPD4821 Approved
0.679 Remote Similarity NPD4822 Approved
0.679 Remote Similarity NPD4819 Approved
0.6719 Remote Similarity NPD3173 Approved
0.6706 Remote Similarity NPD4249 Approved
0.6628 Remote Similarity NPD4251 Approved
0.6628 Remote Similarity NPD4250 Approved
0.6591 Remote Similarity NPD46 Approved
0.6591 Remote Similarity NPD6698 Approved
0.6585 Remote Similarity NPD4252 Approved
0.6567 Remote Similarity NPD3172 Approved
0.6562 Remote Similarity NPD5343 Approved
0.6548 Remote Similarity NPD5362 Discontinued
0.6543 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6508 Remote Similarity NPD4222 Approved
0.6471 Remote Similarity NPD3195 Phase 2
0.6471 Remote Similarity NPD3194 Approved
0.6471 Remote Similarity NPD3196 Approved
0.6471 Remote Similarity NPD4266 Approved
0.6471 Remote Similarity NPD3730 Approved
0.6471 Remote Similarity NPD3728 Approved
0.6429 Remote Similarity NPD4270 Approved
0.6429 Remote Similarity NPD4269 Approved
0.6404 Remote Similarity NPD7838 Discovery
0.6353 Remote Similarity NPD5332 Approved
0.6353 Remote Similarity NPD5331 Approved
0.6322 Remote Similarity NPD5786 Approved
0.631 Remote Similarity NPD4790 Discontinued
0.6264 Remote Similarity NPD5778 Approved
0.6264 Remote Similarity NPD5779 Approved
0.625 Remote Similarity NPD39 Approved
0.625 Remote Similarity NPD3174 Discontinued
0.6235 Remote Similarity NPD6435 Approved
0.622 Remote Similarity NPD4756 Discovery
0.6207 Remote Similarity NPD5363 Approved
0.6154 Remote Similarity NPD7637 Suspended
0.6118 Remote Similarity NPD5369 Approved
0.6111 Remote Similarity NPD69 Approved
0.6111 Remote Similarity NPD5370 Suspended
0.6111 Remote Similarity NPD9119 Approved
0.6105 Remote Similarity NPD4225 Approved
0.6098 Remote Similarity NPD819 Approved
0.6098 Remote Similarity NPD818 Approved
0.6094 Remote Similarity NPD6097 Approved
0.6094 Remote Similarity NPD6096 Approved
0.6064 Remote Similarity NPD7839 Suspended
0.6061 Remote Similarity NPD622 Approved
0.6044 Remote Similarity NPD5785 Approved
0.6029 Remote Similarity NPD29 Approved
0.6029 Remote Similarity NPD6927 Phase 3
0.6029 Remote Similarity NPD28 Approved
0.6 Remote Similarity NPD5368 Approved
0.5978 Remote Similarity NPD4810 Clinical (unspecified phase)
0.5977 Remote Similarity NPD6110 Phase 1
0.5972 Remote Similarity NPD9118 Approved
0.5938 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5938 Remote Similarity NPD5326 Phase 3
0.5934 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5934 Remote Similarity NPD6101 Approved
0.5909 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5895 Remote Similarity NPD4792 Clinical (unspecified phase)
0.5844 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5843 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5843 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5825 Remote Similarity NPD6421 Discontinued
0.5821 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5816 Remote Similarity NPD5344 Discontinued
0.5806 Remote Similarity NPD6411 Approved
0.5789 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5769 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5758 Remote Similarity NPD4265 Approved
0.5682 Remote Similarity NPD5209 Approved
0.5673 Remote Similarity NPD6371 Approved
0.5658 Remote Similarity NPD368 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