Structure

Physi-Chem Properties

Molecular Weight:  293.16
Volume:  303.791
LogP:  2.232
LogD:  2.071
LogS:  -1.743
# Rotatable Bonds:  7
TPSA:  62.91
# H-Bond Aceptor:  5
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.817
Synthetic Accessibility Score:  3.483
Fsp3:  0.562
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:  -4.681
MDCK Permeability:  4.967642234987579e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  0.064
Human Intestinal Absorption (HIA):  0.057
20% Bioavailability (F20%):  0.018
30% Bioavailability (F30%):  0.504

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.981
Plasma Protein Binding (PPB):  64.61235809326172%
Volume Distribution (VD):  1.844
Pgp-substrate:  37.13425827026367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.029
CYP1A2-substrate:  0.116
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.661
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.126
CYP2D6-inhibitor:  0.595
CYP2D6-substrate:  0.884
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.277

ADMET: Excretion

Clearance (CL):  13.282
Half-life (T1/2):  0.902

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.788
Drug-inuced Liver Injury (DILI):  0.083
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.029
Maximum Recommended Daily Dose:  0.648
Skin Sensitization:  0.92
Carcinogencity:  0.9
Eye Corrosion:  0.019
Eye Irritation:  0.024
Respiratory Toxicity:  0.67

Download Data

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

  Natural Product: NPC130436

Natural Product ID:  NPC130436
Common Name*:   Pandamarilactonine-H
IUPAC Name:   methyl 2-[(2S)-1-[(4E)-4-(4-methyl-5-oxofuran-2-ylidene)butyl]pyrrolidin-2-yl]acetate
Synonyms:   Pandamarilactonine-H
Standard InCHIKey:  NJJCMBJNEBNBQQ-PZMUVPOTSA-N
Standard InCHI:  InChI=1S/C16H23NO4/c1-12-10-14(21-16(12)19)7-3-4-8-17-9-5-6-13(17)11-15(18)20-2/h7,10,13H,3-6,8-9,11H2,1-2H3/b14-7+/t13-/m0/s1
SMILES:  CC1=C/C(=CCCCN2CCC[C@H]2CC(=O)OC)/OC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1215879
PubChem CID:   46919588
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
NPO2146 Pandanus amaryllifolius Species Pandanaceae Eukaryota roots n.a. n.a. PMID[20701299]
NPO2146 Pandanus amaryllifolius Species Pandanaceae 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
NPT81 Cell Line A549 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[536328]
NPT139 Cell Line HT-29 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[536328]
NPT393 Cell Line HCT-116 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[536328]

☑ 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 NPC130436 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 NPC469861
1.0 High Similarity NPC469860
0.7143 Intermediate Similarity NPC150041
0.7093 Intermediate Similarity NPC252503
0.7087 Intermediate Similarity NPC133420
0.7009 Intermediate Similarity NPC47857
0.7009 Intermediate Similarity NPC168758
0.7009 Intermediate Similarity NPC181510
0.7009 Intermediate Similarity NPC58281
0.7 Intermediate Similarity NPC476344
0.699 Remote Similarity NPC199831
0.699 Remote Similarity NPC474828
0.699 Remote Similarity NPC68001
0.699 Remote Similarity NPC474827
0.6966 Remote Similarity NPC68156
0.6881 Remote Similarity NPC193471
0.6881 Remote Similarity NPC130124
0.6837 Remote Similarity NPC72183
0.6837 Remote Similarity NPC110875
0.6837 Remote Similarity NPC299808
0.6837 Remote Similarity NPC118844
0.6813 Remote Similarity NPC471768
0.6792 Remote Similarity NPC271562
0.6759 Remote Similarity NPC469603
0.6737 Remote Similarity NPC296589
0.6729 Remote Similarity NPC474099
0.6699 Remote Similarity NPC26597
0.6667 Remote Similarity NPC52820
0.6667 Remote Similarity NPC6271
0.6667 Remote Similarity NPC241426
0.6637 Remote Similarity NPC106791
0.6637 Remote Similarity NPC201889
0.6637 Remote Similarity NPC284656
0.6637 Remote Similarity NPC174463
0.6604 Remote Similarity NPC64168
0.6591 Remote Similarity NPC84038
0.6588 Remote Similarity NPC248125
0.6556 Remote Similarity NPC469414
0.6556 Remote Similarity NPC329826
0.6522 Remote Similarity NPC11379
0.6522 Remote Similarity NPC230849
0.6517 Remote Similarity NPC474705
0.6509 Remote Similarity NPC173690
0.6509 Remote Similarity NPC80439
0.6509 Remote Similarity NPC279833
0.6505 Remote Similarity NPC150967
0.6491 Remote Similarity NPC235625
0.6484 Remote Similarity NPC123360
0.6465 Remote Similarity NPC81195
0.6449 Remote Similarity NPC469604
0.6437 Remote Similarity NPC218477
0.6415 Remote Similarity NPC474244
0.6415 Remote Similarity NPC473289
0.6396 Remote Similarity NPC316984
0.6396 Remote Similarity NPC30911
0.6389 Remote Similarity NPC93179
0.6364 Remote Similarity NPC470693
0.6339 Remote Similarity NPC43648
0.6322 Remote Similarity NPC203335
0.6316 Remote Similarity NPC277341
0.6316 Remote Similarity NPC226982
0.631 Remote Similarity NPC14437
0.631 Remote Similarity NPC151648
0.631 Remote Similarity NPC270412
0.6296 Remote Similarity NPC44514
0.6293 Remote Similarity NPC471261
0.6289 Remote Similarity NPC475975
0.6279 Remote Similarity NPC220766
0.6264 Remote Similarity NPC476355
0.626 Remote Similarity NPC120335
0.625 Remote Similarity NPC329401
0.625 Remote Similarity NPC287705
0.625 Remote Similarity NPC96272
0.625 Remote Similarity NPC147238
0.625 Remote Similarity NPC477987
0.6238 Remote Similarity NPC159568
0.6237 Remote Similarity NPC10572
0.6235 Remote Similarity NPC68110
0.6235 Remote Similarity NPC132243
0.6226 Remote Similarity NPC474985
0.6222 Remote Similarity NPC186531
0.6216 Remote Similarity NPC298484
0.6214 Remote Similarity NPC313265
0.6207 Remote Similarity NPC191233
0.62 Remote Similarity NPC475739
0.6196 Remote Similarity NPC478192
0.6196 Remote Similarity NPC478191
0.6196 Remote Similarity NPC478196
0.6196 Remote Similarity NPC478193
0.6196 Remote Similarity NPC478195
0.6196 Remote Similarity NPC478194
0.618 Remote Similarity NPC232812
0.6168 Remote Similarity NPC188785
0.6167 Remote Similarity NPC469999
0.6163 Remote Similarity NPC173409
0.6163 Remote Similarity NPC53136
0.6154 Remote Similarity NPC287878
0.6154 Remote Similarity NPC138534
0.6154 Remote Similarity NPC477986
0.6148 Remote Similarity NPC173173
0.6147 Remote Similarity NPC75523
0.6146 Remote Similarity NPC42470
0.6136 Remote Similarity NPC21998
0.6136 Remote Similarity NPC194871
0.6121 Remote Similarity NPC65045
0.6121 Remote Similarity NPC469997
0.6118 Remote Similarity NPC217537
0.6111 Remote Similarity NPC37929
0.6111 Remote Similarity NPC64234
0.6111 Remote Similarity NPC67183
0.6095 Remote Similarity NPC476449
0.6092 Remote Similarity NPC131174
0.6092 Remote Similarity NPC133904
0.6087 Remote Similarity NPC294434
0.6087 Remote Similarity NPC474758
0.6087 Remote Similarity NPC140287
0.6087 Remote Similarity NPC117746
0.6087 Remote Similarity NPC470994
0.6087 Remote Similarity NPC15499
0.6087 Remote Similarity NPC259599
0.6082 Remote Similarity NPC73310
0.6082 Remote Similarity NPC94875
0.6082 Remote Similarity NPC475159
0.6082 Remote Similarity NPC473712
0.6082 Remote Similarity NPC473780
0.6082 Remote Similarity NPC180363
0.6082 Remote Similarity NPC65930
0.6082 Remote Similarity NPC473529
0.6082 Remote Similarity NPC329829
0.6082 Remote Similarity NPC131002
0.6082 Remote Similarity NPC173609
0.6082 Remote Similarity NPC11332
0.6082 Remote Similarity NPC145914
0.6071 Remote Similarity NPC133600
0.6067 Remote Similarity NPC470256
0.6064 Remote Similarity NPC473825
0.6064 Remote Similarity NPC57744
0.6061 Remote Similarity NPC474424
0.6055 Remote Similarity NPC469895
0.605 Remote Similarity NPC23963
0.6048 Remote Similarity NPC477988
0.6047 Remote Similarity NPC44343
0.6047 Remote Similarity NPC155849
0.6047 Remote Similarity NPC210303
0.6047 Remote Similarity NPC179087
0.6044 Remote Similarity NPC112983
0.6044 Remote Similarity NPC162571
0.6044 Remote Similarity NPC163003
0.6038 Remote Similarity NPC265662
0.6033 Remote Similarity NPC26285
0.602 Remote Similarity NPC475947
0.602 Remote Similarity NPC144415
0.602 Remote Similarity NPC253801
0.6018 Remote Similarity NPC195435
0.6018 Remote Similarity NPC196073
0.6 Remote Similarity NPC108816
0.6 Remote Similarity NPC79756
0.6 Remote Similarity NPC476591
0.6 Remote Similarity NPC494
0.6 Remote Similarity NPC93763
0.6 Remote Similarity NPC128276
0.6 Remote Similarity NPC88877
0.5978 Remote Similarity NPC146583
0.5976 Remote Similarity NPC173157
0.5962 Remote Similarity NPC304897
0.596 Remote Similarity NPC156804
0.596 Remote Similarity NPC163093
0.595 Remote Similarity NPC323168
0.595 Remote Similarity NPC293550
0.595 Remote Similarity NPC477990
0.595 Remote Similarity NPC477989
0.595 Remote Similarity NPC111162
0.5943 Remote Similarity NPC301596
0.5943 Remote Similarity NPC172998
0.5943 Remote Similarity NPC299396
0.5943 Remote Similarity NPC175614
0.5938 Remote Similarity NPC270126
0.5938 Remote Similarity NPC178277
0.5934 Remote Similarity NPC315285
0.5922 Remote Similarity NPC474098
0.5922 Remote Similarity NPC475995
0.5922 Remote Similarity NPC17143
0.5922 Remote Similarity NPC47230
0.592 Remote Similarity NPC215507
0.5917 Remote Similarity NPC470000
0.5914 Remote Similarity NPC470686
0.5913 Remote Similarity NPC275100
0.5913 Remote Similarity NPC474497
0.5909 Remote Similarity NPC182794
0.5909 Remote Similarity NPC470688
0.5909 Remote Similarity NPC471556
0.5904 Remote Similarity NPC86948
0.59 Remote Similarity NPC77871
0.59 Remote Similarity NPC215364
0.59 Remote Similarity NPC100921
0.59 Remote Similarity NPC1083
0.59 Remote Similarity NPC473671
0.59 Remote Similarity NPC477014
0.59 Remote Similarity NPC292809
0.59 Remote Similarity NPC322529

  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 NPC130436 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
0.6396 Remote Similarity NPD2204 Approved
0.6374 Remote Similarity NPD1452 Discontinued
0.631 Remote Similarity NPD9418 Clinical (unspecified phase)
0.6118 Remote Similarity NPD3205 Discontinued
0.6055 Remote Similarity NPD2258 Approved
0.6055 Remote Similarity NPD2259 Approved
0.5895 Remote Similarity NPD4756 Discovery
0.5794 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5758 Remote Similarity NPD5209 Approved
0.5758 Remote Similarity NPD2567 Approved
0.5758 Remote Similarity NPD2569 Approved
0.5726 Remote Similarity NPD1376 Discontinued
0.5652 Remote Similarity NPD2696 Approved
0.5652 Remote Similarity NPD2695 Approved
0.5652 Remote Similarity NPD2697 Approved
0.5652 Remote Similarity NPD2694 Approved
0.56 Remote Similarity NPD4752 Clinical (unspecified phase)

  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