Structure

Physi-Chem Properties

Molecular Weight:  256.09
Volume:  243.827
LogP:  0.676
LogD:  0.833
LogS:  -1.059
# Rotatable Bonds:  3
TPSA:  82.06
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.712
Synthetic Accessibility Score:  4.693
Fsp3:  0.667
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:  -5.066
MDCK Permeability:  5.228189911576919e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.061
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.821
Plasma Protein Binding (PPB):  20.053661346435547%
Volume Distribution (VD):  0.898
Pgp-substrate:  62.950592041015625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.08
CYP1A2-substrate:  0.071
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.318
CYP2C9-inhibitor:  0.021
CYP2C9-substrate:  0.065
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.141
CYP3A4-inhibitor:  0.075
CYP3A4-substrate:  0.269

ADMET: Excretion

Clearance (CL):  8.376
Half-life (T1/2):  0.899

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.579
Drug-inuced Liver Injury (DILI):  0.23
AMES Toxicity:  0.042
Rat Oral Acute Toxicity:  0.737
Maximum Recommended Daily Dose:  0.661
Skin Sensitization:  0.51
Carcinogencity:  0.73
Eye Corrosion:  0.024
Eye Irritation:  0.083
Respiratory Toxicity:  0.456

Download Data

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

  Natural Product: NPC297440

Natural Product ID:  NPC297440
Common Name*:   Angiopterlactone A
IUPAC Name:   (2S,3S)-3-[(2R,3R)-2-[(1S)-1-hydroxyethyl]-5-oxooxolan-3-yl]oxy-2-methyl-2,3-dihydropyran-6-one
Synonyms:   Angiopterlactone A
Standard InCHIKey:  BRMROXXXIVEVKO-DADSOTLSSA-N
Standard InCHI:  InChI=1S/C12H16O6/c1-6(13)12-9(5-11(15)18-12)17-8-3-4-10(14)16-7(8)2/h3-4,6-9,12-13H,5H2,1-2H3/t6-,7-,8-,9+,12+/m0/s1
SMILES:  O=C1C=C[C@@H]([C@@H](O1)C)O[C@@H]1CC(=O)O[C@@H]1[C@@H](O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL564792
PubChem CID:   44140025
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
NPO24883 Angiopteris caudatiformis Species Marattiaceae Eukaryota n.a. n.a. n.a. PMID[19371069]
NPO24883 Angiopteris caudatiformis Species Marattiaceae 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
NPT165 Cell Line HeLa Homo sapiens IC50 = 68800.0 nM PMID[473159]

☑ 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 NPC297440 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
0.8701 High Similarity NPC473948
0.8214 Intermediate Similarity NPC474251
0.8052 Intermediate Similarity NPC475982
0.8023 Intermediate Similarity NPC112685
0.8 Intermediate Similarity NPC161038
0.7907 Intermediate Similarity NPC21469
0.7901 Intermediate Similarity NPC190400
0.7901 Intermediate Similarity NPC49392
0.7895 Intermediate Similarity NPC201356
0.7865 Intermediate Similarity NPC473619
0.7865 Intermediate Similarity NPC274075
0.7831 Intermediate Similarity NPC99651
0.7826 Intermediate Similarity NPC477921
0.7816 Intermediate Similarity NPC478112
0.7816 Intermediate Similarity NPC309211
0.7816 Intermediate Similarity NPC279267
0.7816 Intermediate Similarity NPC69082
0.7805 Intermediate Similarity NPC275530
0.7805 Intermediate Similarity NPC474026
0.7805 Intermediate Similarity NPC475711
0.7778 Intermediate Similarity NPC473321
0.7765 Intermediate Similarity NPC310450
0.7765 Intermediate Similarity NPC11383
0.7765 Intermediate Similarity NPC474959
0.7765 Intermediate Similarity NPC475046
0.7763 Intermediate Similarity NPC96414
0.7753 Intermediate Similarity NPC87306
0.7753 Intermediate Similarity NPC280612
0.7753 Intermediate Similarity NPC130359
0.7753 Intermediate Similarity NPC477011
0.7753 Intermediate Similarity NPC14901
0.7727 Intermediate Similarity NPC473248
0.7727 Intermediate Similarity NPC178215
0.7722 Intermediate Similarity NPC202011
0.7717 Intermediate Similarity NPC477922
0.7717 Intermediate Similarity NPC471142
0.7711 Intermediate Similarity NPC473471
0.7711 Intermediate Similarity NPC248775
0.7701 Intermediate Similarity NPC103284
0.7701 Intermediate Similarity NPC1083
0.7701 Intermediate Similarity NPC66346
0.7701 Intermediate Similarity NPC223871
0.7701 Intermediate Similarity NPC473669
0.7701 Intermediate Similarity NPC477018
0.7701 Intermediate Similarity NPC473478
0.7701 Intermediate Similarity NPC283085
0.7701 Intermediate Similarity NPC100921
0.7701 Intermediate Similarity NPC107986
0.7701 Intermediate Similarity NPC182383
0.7701 Intermediate Similarity NPC286338
0.7701 Intermediate Similarity NPC82795
0.7701 Intermediate Similarity NPC231009
0.7701 Intermediate Similarity NPC132496
0.7701 Intermediate Similarity NPC473651
0.7701 Intermediate Similarity NPC110710
0.7692 Intermediate Similarity NPC295204
0.7692 Intermediate Similarity NPC288240
0.7692 Intermediate Similarity NPC162205
0.7692 Intermediate Similarity NPC273579
0.7683 Intermediate Similarity NPC301207
0.7683 Intermediate Similarity NPC127118
0.7683 Intermediate Similarity NPC209113
0.7674 Intermediate Similarity NPC284472
0.7674 Intermediate Similarity NPC286770
0.7674 Intermediate Similarity NPC253801
0.7674 Intermediate Similarity NPC229799
0.7667 Intermediate Similarity NPC473455
0.7662 Intermediate Similarity NPC276299
0.766 Intermediate Similarity NPC471144
0.7647 Intermediate Similarity NPC150502
0.764 Intermediate Similarity NPC21208
0.764 Intermediate Similarity NPC280621
0.764 Intermediate Similarity NPC473715
0.764 Intermediate Similarity NPC48338
0.764 Intermediate Similarity NPC40376
0.764 Intermediate Similarity NPC89001
0.764 Intermediate Similarity NPC20339
0.764 Intermediate Similarity NPC233551
0.7619 Intermediate Similarity NPC473981
0.7619 Intermediate Similarity NPC473980
0.7619 Intermediate Similarity NPC470149
0.7619 Intermediate Similarity NPC470148
0.7619 Intermediate Similarity NPC180725
0.7614 Intermediate Similarity NPC134885
0.7614 Intermediate Similarity NPC62118
0.7614 Intermediate Similarity NPC231096
0.7614 Intermediate Similarity NPC134807
0.7614 Intermediate Similarity NPC219498
0.7614 Intermediate Similarity NPC107717
0.7614 Intermediate Similarity NPC171174
0.7614 Intermediate Similarity NPC134865
0.7614 Intermediate Similarity NPC142117
0.7614 Intermediate Similarity NPC475581
0.7614 Intermediate Similarity NPC240695
0.7614 Intermediate Similarity NPC308412
0.7614 Intermediate Similarity NPC114694
0.7614 Intermediate Similarity NPC473687
0.7614 Intermediate Similarity NPC47937
0.7614 Intermediate Similarity NPC232555
0.7614 Intermediate Similarity NPC477010
0.7614 Intermediate Similarity NPC103523
0.7614 Intermediate Similarity NPC210218
0.7614 Intermediate Similarity NPC204686
0.759 Intermediate Similarity NPC176329
0.759 Intermediate Similarity NPC474818
0.759 Intermediate Similarity NPC49302
0.759 Intermediate Similarity NPC51809
0.759 Intermediate Similarity NPC125365
0.7586 Intermediate Similarity NPC163093
0.7558 Intermediate Similarity NPC473780
0.7558 Intermediate Similarity NPC180363
0.7558 Intermediate Similarity NPC473712
0.7558 Intermediate Similarity NPC73310
0.7558 Intermediate Similarity NPC65930
0.7558 Intermediate Similarity NPC11332
0.7558 Intermediate Similarity NPC475159
0.7558 Intermediate Similarity NPC131002
0.7558 Intermediate Similarity NPC329829
0.7558 Intermediate Similarity NPC94875
0.7558 Intermediate Similarity NPC145914
0.7558 Intermediate Similarity NPC473529
0.7556 Intermediate Similarity NPC477017
0.7556 Intermediate Similarity NPC477016
0.7553 Intermediate Similarity NPC40812
0.7532 Intermediate Similarity NPC19769
0.7531 Intermediate Similarity NPC185186
0.7531 Intermediate Similarity NPC327383
0.7529 Intermediate Similarity NPC133226
0.7529 Intermediate Similarity NPC470147
0.7528 Intermediate Similarity NPC154097
0.7528 Intermediate Similarity NPC470401
0.7528 Intermediate Similarity NPC473649
0.7528 Intermediate Similarity NPC159750
0.7526 Intermediate Similarity NPC475871
0.7526 Intermediate Similarity NPC475945
0.75 Intermediate Similarity NPC318481
0.75 Intermediate Similarity NPC470124
0.75 Intermediate Similarity NPC279214
0.75 Intermediate Similarity NPC221095
0.75 Intermediate Similarity NPC477014
0.75 Intermediate Similarity NPC474742
0.75 Intermediate Similarity NPC120398
0.75 Intermediate Similarity NPC477013
0.75 Intermediate Similarity NPC322529
0.75 Intermediate Similarity NPC475912
0.75 Intermediate Similarity NPC11456
0.75 Intermediate Similarity NPC475699
0.75 Intermediate Similarity NPC471567
0.7474 Intermediate Similarity NPC187761
0.7474 Intermediate Similarity NPC83895
0.7473 Intermediate Similarity NPC239517
0.7473 Intermediate Similarity NPC474232
0.7473 Intermediate Similarity NPC473311
0.7471 Intermediate Similarity NPC52923
0.7471 Intermediate Similarity NPC144415
0.7449 Intermediate Similarity NPC203659
0.7447 Intermediate Similarity NPC473859
0.7444 Intermediate Similarity NPC320569
0.7444 Intermediate Similarity NPC169511
0.7444 Intermediate Similarity NPC172821
0.7444 Intermediate Similarity NPC133730
0.7444 Intermediate Similarity NPC151403
0.7444 Intermediate Similarity NPC81045
0.7444 Intermediate Similarity NPC287164
0.7444 Intermediate Similarity NPC171135
0.7444 Intermediate Similarity NPC61257
0.7444 Intermediate Similarity NPC261952
0.7444 Intermediate Similarity NPC153570
0.7444 Intermediate Similarity NPC242364
0.7444 Intermediate Similarity NPC234077
0.7444 Intermediate Similarity NPC191929
0.7444 Intermediate Similarity NPC39754
0.7444 Intermediate Similarity NPC274446
0.7444 Intermediate Similarity NPC100454
0.7423 Intermediate Similarity NPC474747
0.7423 Intermediate Similarity NPC149371
0.7416 Intermediate Similarity NPC477015
0.7416 Intermediate Similarity NPC469910
0.7416 Intermediate Similarity NPC278283
0.7412 Intermediate Similarity NPC475210
0.7396 Intermediate Similarity NPC475949
0.7396 Intermediate Similarity NPC288876
0.7391 Intermediate Similarity NPC184463
0.7391 Intermediate Similarity NPC327760
0.7391 Intermediate Similarity NPC30515
0.7386 Intermediate Similarity NPC38569
0.7386 Intermediate Similarity NPC32676
0.7386 Intermediate Similarity NPC163615
0.7386 Intermediate Similarity NPC156804
0.7363 Intermediate Similarity NPC473504
0.7363 Intermediate Similarity NPC139418
0.7363 Intermediate Similarity NPC474032
0.7363 Intermediate Similarity NPC91067
0.7363 Intermediate Similarity NPC40066
0.7363 Intermediate Similarity NPC93794
0.7363 Intermediate Similarity NPC20621
0.7363 Intermediate Similarity NPC81778
0.7363 Intermediate Similarity NPC42598
0.7363 Intermediate Similarity NPC318963
0.7356 Intermediate Similarity NPC475690

  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 NPC297440 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
0.7125 Intermediate Similarity NPD4247 Clinical (unspecified phase)
0.6979 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6915 Remote Similarity NPD6698 Approved
0.6915 Remote Similarity NPD46 Approved
0.6842 Remote Similarity NPD7983 Approved
0.6768 Remote Similarity NPD4225 Approved
0.6739 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6635 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6562 Remote Similarity NPD5785 Approved
0.6562 Remote Similarity NPD7838 Discovery
0.6449 Remote Similarity NPD6371 Approved
0.6429 Remote Similarity NPD5779 Approved
0.6429 Remote Similarity NPD5778 Approved
0.6383 Remote Similarity NPD5363 Approved
0.6316 Remote Similarity NPD8513 Phase 3
0.6316 Remote Similarity NPD5786 Approved
0.6275 Remote Similarity NPD8029 Clinical (unspecified phase)
0.625 Remote Similarity NPD7115 Discovery
0.6239 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6238 Remote Similarity NPD7839 Suspended
0.6203 Remote Similarity NPD8959 Approved
0.6196 Remote Similarity NPD4252 Approved
0.6174 Remote Similarity NPD8516 Approved
0.6174 Remote Similarity NPD8517 Approved
0.6174 Remote Similarity NPD8515 Approved
0.6173 Remote Similarity NPD4246 Clinical (unspecified phase)
0.617 Remote Similarity NPD6110 Phase 1
0.6146 Remote Similarity NPD4249 Approved
0.6145 Remote Similarity NPD3197 Phase 1
0.6125 Remote Similarity NPD585 Clinical (unspecified phase)
0.6125 Remote Similarity NPD6109 Phase 1
0.6125 Remote Similarity NPD69 Approved
0.6125 Remote Similarity NPD9119 Approved
0.6111 Remote Similarity NPD6686 Approved
0.6082 Remote Similarity NPD4250 Approved
0.6082 Remote Similarity NPD4251 Approved
0.6068 Remote Similarity NPD7642 Approved
0.6068 Remote Similarity NPD7830 Approved
0.6068 Remote Similarity NPD7829 Approved
0.6064 Remote Similarity NPD4270 Approved
0.6064 Remote Similarity NPD4269 Approved
0.6064 Remote Similarity NPD5209 Approved
0.6022 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6 Remote Similarity NPD9118 Approved
0.6 Remote Similarity NPD7637 Suspended
0.6 Remote Similarity NPD7154 Phase 3
0.6 Remote Similarity NPD5344 Discontinued
0.596 Remote Similarity NPD5764 Clinical (unspecified phase)
0.596 Remote Similarity NPD6101 Approved
0.5957 Remote Similarity NPD5369 Approved
0.5938 Remote Similarity NPD6400 Clinical (unspecified phase)
0.593 Remote Similarity NPD896 Approved
0.593 Remote Similarity NPD897 Approved
0.593 Remote Similarity NPD898 Approved
0.5917 Remote Similarity NPD8074 Phase 3
0.5895 Remote Similarity NPD6435 Approved
0.5893 Remote Similarity NPD6053 Discontinued
0.5882 Remote Similarity NPD5282 Discontinued
0.5876 Remote Similarity NPD1694 Approved
0.587 Remote Similarity NPD4756 Discovery
0.5842 Remote Similarity NPD4810 Clinical (unspecified phase)
0.5842 Remote Similarity NPD6411 Approved
0.5833 Remote Similarity NPD8961 Approved
0.5806 Remote Similarity NPD4271 Approved
0.5806 Remote Similarity NPD4268 Approved
0.5804 Remote Similarity NPD2204 Approved
0.58 Remote Similarity NPD1695 Approved
0.58 Remote Similarity NPD5370 Suspended
0.5789 Remote Similarity NPD3173 Approved
0.5769 Remote Similarity NPD72 Approved
0.5769 Remote Similarity NPD9009 Approved
0.5769 Remote Similarity NPD65 Approved
0.5769 Remote Similarity NPD9011 Approved
0.5769 Remote Similarity NPD9008 Approved
0.5769 Remote Similarity NPD9010 Approved
0.5769 Remote Similarity NPD66 Approved
0.5769 Remote Similarity NPD8960 Approved
0.5769 Remote Similarity NPD64 Approved
0.5769 Remote Similarity NPD9007 Approved
0.5763 Remote Similarity NPD8444 Approved
0.5748 Remote Similarity NPD7966 Clinical (unspecified phase)
0.5702 Remote Similarity NPD8451 Approved
0.5684 Remote Similarity NPD4821 Approved
0.5684 Remote Similarity NPD4819 Approved
0.5684 Remote Similarity NPD4820 Approved
0.5684 Remote Similarity NPD4822 Approved
0.5684 Remote Similarity NPD5368 Approved
0.5678 Remote Similarity NPD6319 Approved
0.5676 Remote Similarity NPD5345 Clinical (unspecified phase)
0.567 Remote Similarity NPD5362 Discontinued
0.566 Remote Similarity NPD7638 Approved
0.5656 Remote Similarity NPD8448 Approved
0.5641 Remote Similarity NPD7641 Discontinued
0.5638 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5619 Remote Similarity NPD4228 Discovery
0.5607 Remote Similarity NPD6648 Approved
0.5607 Remote Similarity NPD7640 Approved
0.5607 Remote Similarity NPD7639 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