Structure

Physi-Chem Properties

Molecular Weight:  220.05
Volume:  200.763
LogP:  0.243
LogD:  -1.296
LogS:  -0.852
# Rotatable Bonds:  2
TPSA:  63.6
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.689
Synthetic Accessibility Score:  4.569
Fsp3:  0.778
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.519
MDCK Permeability:  2.67153973254608e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.026
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.964
Plasma Protein Binding (PPB):  39.972957611083984%
Volume Distribution (VD):  1.642
Pgp-substrate:  66.75253295898438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.639
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.865
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.155
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.306
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.205

ADMET: Excretion

Clearance (CL):  6.578
Half-life (T1/2):  0.94

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.282
Drug-inuced Liver Injury (DILI):  0.897
AMES Toxicity:  0.244
Rat Oral Acute Toxicity:  0.858
Maximum Recommended Daily Dose:  0.027
Skin Sensitization:  0.298
Carcinogencity:  0.228
Eye Corrosion:  0.582
Eye Irritation:  0.204
Respiratory Toxicity:  0.23

Download Data

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

  Natural Product: NPC121374

Natural Product ID:  NPC121374
Common Name*:   Chlorohydroaspyrone B
IUPAC Name:   (2R,3S)-5-[(1S,2S)-2-chloro-1-hydroxypropyl]-3-hydroxy-2-methyl-2,3-dihydropyran-6-one
Synonyms:  
Standard InCHIKey:  RFRJSDLXLVSACH-UGSJSWHKSA-N
Standard InCHI:  InChI=1S/C9H13ClO4/c1-4(10)8(12)6-3-7(11)5(2)14-9(6)13/h3-5,7-8,11-12H,1-2H3/t4-,5+,7-,8+/m0/s1
SMILES:  C[C@@H]([C@H](C1=C[C@H](O)[C@H](OC1=O)C)O)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL496283
PubChem CID:   25016145
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives
          • [CHEMONTID:0001211] Dihydropyranones

*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
NPO32971 exophiala sp. Species Herpotrichiellaceae Eukaryota n.a. n.a. n.a. PMID[18661951]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 62.5 ug.mL-1 PMID[540521]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 125.0 ug.mL-1 PMID[540521]

☑ 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 NPC121374 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
0.9211 High Similarity NPC28049
0.8289 Intermediate Similarity NPC202011
0.7875 Intermediate Similarity NPC161038
0.7683 Intermediate Similarity NPC275530
0.7632 Intermediate Similarity NPC273600
0.7561 Intermediate Similarity NPC470705
0.7532 Intermediate Similarity NPC201356
0.7468 Intermediate Similarity NPC475982
0.7442 Intermediate Similarity NPC474959
0.7442 Intermediate Similarity NPC475046
0.7442 Intermediate Similarity NPC11383
0.7442 Intermediate Similarity NPC310450
0.7403 Intermediate Similarity NPC96414
0.7403 Intermediate Similarity NPC470123
0.7356 Intermediate Similarity NPC284472
0.7356 Intermediate Similarity NPC286770
0.7356 Intermediate Similarity NPC229799
0.7349 Intermediate Similarity NPC301207
0.7326 Intermediate Similarity NPC150502
0.7326 Intermediate Similarity NPC297440
0.7294 Intermediate Similarity NPC99651
0.7262 Intermediate Similarity NPC474818
0.7262 Intermediate Similarity NPC176329
0.7262 Intermediate Similarity NPC125365
0.7262 Intermediate Similarity NPC49302
0.7262 Intermediate Similarity NPC51809
0.7229 Intermediate Similarity NPC478192
0.7229 Intermediate Similarity NPC478191
0.7229 Intermediate Similarity NPC478196
0.7229 Intermediate Similarity NPC478195
0.7229 Intermediate Similarity NPC478194
0.7229 Intermediate Similarity NPC478193
0.72 Intermediate Similarity NPC302564
0.7179 Intermediate Similarity NPC19769
0.7176 Intermediate Similarity NPC221095
0.7176 Intermediate Similarity NPC318481
0.7176 Intermediate Similarity NPC279214
0.7176 Intermediate Similarity NPC473471
0.7143 Intermediate Similarity NPC209113
0.7143 Intermediate Similarity NPC203277
0.7143 Intermediate Similarity NPC127118
0.7108 Intermediate Similarity NPC476590
0.7108 Intermediate Similarity NPC114727
0.7093 Intermediate Similarity NPC199134
0.7093 Intermediate Similarity NPC286816
0.7089 Intermediate Similarity NPC475555
0.7089 Intermediate Similarity NPC276299
0.7089 Intermediate Similarity NPC475675
0.7059 Intermediate Similarity NPC475711
0.7024 Intermediate Similarity NPC473948
0.7 Intermediate Similarity NPC470124
0.6977 Remote Similarity NPC279532
0.6962 Remote Similarity NPC478099
0.6962 Remote Similarity NPC478098
0.6962 Remote Similarity NPC282760
0.6941 Remote Similarity NPC256640
0.6941 Remote Similarity NPC205615
0.6941 Remote Similarity NPC16279
0.6923 Remote Similarity NPC68110
0.6914 Remote Similarity NPC63873
0.6914 Remote Similarity NPC238223
0.6905 Remote Similarity NPC315843
0.6905 Remote Similarity NPC107654
0.6905 Remote Similarity NPC326504
0.6875 Remote Similarity NPC478101
0.6867 Remote Similarity NPC293114
0.6835 Remote Similarity NPC470808
0.6824 Remote Similarity NPC260396
0.6824 Remote Similarity NPC473582
0.6813 Remote Similarity NPC475034
0.679 Remote Similarity NPC132286
0.679 Remote Similarity NPC25298
0.679 Remote Similarity NPC478100
0.679 Remote Similarity NPC478097
0.6782 Remote Similarity NPC248775
0.6778 Remote Similarity NPC161045
0.6778 Remote Similarity NPC44261
0.6778 Remote Similarity NPC16488
0.6753 Remote Similarity NPC97570
0.675 Remote Similarity NPC476589
0.6744 Remote Similarity NPC49392
0.6744 Remote Similarity NPC190400
0.6744 Remote Similarity NPC68819
0.6742 Remote Similarity NPC474980
0.6739 Remote Similarity NPC315395
0.6739 Remote Similarity NPC316426
0.6739 Remote Similarity NPC469910
0.6737 Remote Similarity NPC180617
0.6735 Remote Similarity NPC245521
0.6711 Remote Similarity NPC135863
0.6709 Remote Similarity NPC2328
0.6709 Remote Similarity NPC473737
0.6706 Remote Similarity NPC473489
0.6705 Remote Similarity NPC473947
0.6705 Remote Similarity NPC470149
0.6705 Remote Similarity NPC180725
0.6705 Remote Similarity NPC470148
0.6703 Remote Similarity NPC474251
0.6667 Remote Similarity NPC469692
0.6667 Remote Similarity NPC472072
0.6667 Remote Similarity NPC469645
0.6667 Remote Similarity NPC146811
0.6667 Remote Similarity NPC26223
0.6667 Remote Similarity NPC316185
0.6667 Remote Similarity NPC272267
0.6667 Remote Similarity NPC475037
0.6667 Remote Similarity NPC37382
0.6667 Remote Similarity NPC474026
0.6667 Remote Similarity NPC133098
0.6632 Remote Similarity NPC474232
0.6632 Remote Similarity NPC274075
0.663 Remote Similarity NPC182383
0.663 Remote Similarity NPC11804
0.663 Remote Similarity NPC470755
0.6629 Remote Similarity NPC470147
0.6629 Remote Similarity NPC133226
0.6629 Remote Similarity NPC47653
0.6627 Remote Similarity NPC151481
0.6627 Remote Similarity NPC130618
0.6625 Remote Similarity NPC308457
0.6625 Remote Similarity NPC25747
0.6625 Remote Similarity NPC148233
0.6598 Remote Similarity NPC121825
0.6596 Remote Similarity NPC476803
0.6596 Remote Similarity NPC287089
0.6593 Remote Similarity NPC315559
0.6591 Remote Similarity NPC477314
0.6588 Remote Similarity NPC284006
0.6585 Remote Similarity NPC203335
0.6585 Remote Similarity NPC122627
0.6582 Remote Similarity NPC263732
0.6582 Remote Similarity NPC26810
0.6582 Remote Similarity NPC151648
0.6559 Remote Similarity NPC47937
0.6559 Remote Similarity NPC472009
0.6548 Remote Similarity NPC59558
0.6542 Remote Similarity NPC258711
0.6542 Remote Similarity NPC35069
0.6526 Remote Similarity NPC14901
0.6526 Remote Similarity NPC79027
0.6526 Remote Similarity NPC130359
0.6522 Remote Similarity NPC70424
0.6522 Remote Similarity NPC30915
0.6522 Remote Similarity NPC163093
0.6522 Remote Similarity NPC469809
0.6522 Remote Similarity NPC475035
0.6522 Remote Similarity NPC474865
0.6522 Remote Similarity NPC243618
0.6522 Remote Similarity NPC158756
0.6517 Remote Similarity NPC475210
0.6512 Remote Similarity NPC477422
0.6506 Remote Similarity NPC287705
0.65 Remote Similarity NPC475073
0.6495 Remote Similarity NPC29798
0.6495 Remote Similarity NPC282644
0.6494 Remote Similarity NPC293437
0.6494 Remote Similarity NPC249850
0.6489 Remote Similarity NPC178215
0.6489 Remote Similarity NPC472007
0.6484 Remote Similarity NPC329829
0.6484 Remote Similarity NPC131002
0.6484 Remote Similarity NPC94875
0.6484 Remote Similarity NPC8161
0.6484 Remote Similarity NPC145914
0.6484 Remote Similarity NPC26624
0.6484 Remote Similarity NPC473529
0.6484 Remote Similarity NPC313677
0.6484 Remote Similarity NPC11332
0.6484 Remote Similarity NPC65930
0.6484 Remote Similarity NPC475159
0.6484 Remote Similarity NPC473712
0.6484 Remote Similarity NPC473780
0.6484 Remote Similarity NPC73310
0.6484 Remote Similarity NPC180363
0.6477 Remote Similarity NPC474278
0.6465 Remote Similarity NPC477921
0.6463 Remote Similarity NPC124586
0.6463 Remote Similarity NPC248125
0.6458 Remote Similarity NPC473311
0.6456 Remote Similarity NPC79756
0.6456 Remote Similarity NPC321919
0.6456 Remote Similarity NPC81896
0.6452 Remote Similarity NPC132496
0.6452 Remote Similarity NPC231009
0.6452 Remote Similarity NPC471567
0.6452 Remote Similarity NPC477013
0.6452 Remote Similarity NPC120398
0.6452 Remote Similarity NPC110710
0.6452 Remote Similarity NPC286338
0.6452 Remote Similarity NPC21469
0.6452 Remote Similarity NPC103284
0.6452 Remote Similarity NPC473478
0.6452 Remote Similarity NPC1083
0.6452 Remote Similarity NPC473669
0.6452 Remote Similarity NPC107986
0.6452 Remote Similarity NPC283085
0.6452 Remote Similarity NPC223871
0.6452 Remote Similarity NPC477014
0.6452 Remote Similarity NPC82795
0.6452 Remote Similarity NPC473651

  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 NPC121374 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
0.6337 Remote Similarity NPD4225 Approved
0.6289 Remote Similarity NPD46 Approved
0.6289 Remote Similarity NPD6698 Approved
0.6139 Remote Similarity NPD4792 Clinical (unspecified phase)
0.6 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6 Remote Similarity NPD585 Clinical (unspecified phase)
0.6 Remote Similarity NPD69 Approved
0.6 Remote Similarity NPD9119 Approved
0.596 Remote Similarity NPD7838 Discovery
0.59 Remote Similarity NPD7983 Approved
0.5875 Remote Similarity NPD9118 Approved
0.5802 Remote Similarity NPD6109 Phase 1
0.58 Remote Similarity NPD5785 Approved
0.5766 Remote Similarity NPD6371 Approved
0.5761 Remote Similarity NPD4756 Discovery
0.5739 Remote Similarity NPD7115 Discovery
0.5728 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6927 Phase 3
0.5714 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5663 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5636 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5632 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5209 Approved
0.5612 Remote Similarity NPD5363 Approved
0.5607 Remote Similarity NPD5344 Discontinued

  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