Structure

Physi-Chem Properties

Molecular Weight:  383.19
Volume:  382.266
LogP:  3.194
LogD:  3.304
LogS:  -3.417
# Rotatable Bonds:  3
TPSA:  96.71
# H-Bond Aceptor:  5
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.404
Synthetic Accessibility Score:  5.226
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.349
MDCK Permeability:  1.0209525498794392e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.996
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.826
30% Bioavailability (F30%):  0.05

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.467
Plasma Protein Binding (PPB):  56.913978576660156%
Volume Distribution (VD):  1.92
Pgp-substrate:  44.38109588623047%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.241
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.113
CYP2C9-inhibitor:  0.018
CYP2C9-substrate:  0.852
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.384
CYP3A4-inhibitor:  0.063
CYP3A4-substrate:  0.165

ADMET: Excretion

Clearance (CL):  8.437
Half-life (T1/2):  0.566

ADMET: Toxicity

hERG Blockers:  0.11
Human Hepatotoxicity (H-HT):  0.389
Drug-inuced Liver Injury (DILI):  0.204
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.919
Maximum Recommended Daily Dose:  0.996
Skin Sensitization:  0.137
Carcinogencity:  0.929
Eye Corrosion:  0.004
Eye Irritation:  0.017
Respiratory Toxicity:  0.925

Download Data

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

  Natural Product: NPC92829

Natural Product ID:  NPC92829
Common Name*:   Chlorolissoclimide
IUPAC Name:   (3R)-3-[(1S)-2-[(1R,3S,4aS,7S,8aS)-7-chloro-3-hydroxy-5,5,8a-trimethyl-2-methylidene-3,4,4a,6,7,8-hexahydro-1H-naphthalen-1-yl]-1-hydroxyethyl]pyrrolidine-2,5-dione
Synonyms:   Chlorolissoclimide
Standard InCHIKey:  LCBZIVZSFYGPBC-LWHFJPTFSA-N
Standard InCHI:  InChI=1S/C20H30ClNO4/c1-10-13(6-15(24)12-5-17(25)22-18(12)26)20(4)9-11(21)8-19(2,3)16(20)7-14(10)23/h11-16,23-24H,1,5-9H2,2-4H3,(H,22,25,26)/t11-,12+,13-,14-,15-,16-,20+/m0/s1
SMILES:  C=C1[C@H](C[C@@H]([C@H]2CC(=NC2=O)O)O)[C@@]2(C)C[C@H](CC(C)(C)[C@@H]2C[C@@H]1O)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL514096
PubChem CID:   127675
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000218] Pyrrolidines
        • [CHEMONTID:0001158] Pyrrolidones
          • [CHEMONTID:0003031] Pyrrolidine-2-ones

*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
NPO32802 Pleurobranchus forskalii Species Pleurobranchidae Eukaryota n.a. n.a. n.a. PMID[15332867]
NPO18522 Pleurobranchus albiguttatus Species Pleurobranchidae Eukaryota n.a. n.a. n.a. PMID[15332867]
NPO32802 Pleurobranchus forskalii Species Pleurobranchidae Eukaryota n.a. n.a. n.a. PMID[23848233]
NPO32802 Pleurobranchus forskalii Species Pleurobranchidae Eukaryota n.a. n.a. n.a. PMID[8786369]
NPO18522 Pleurobranchus albiguttatus Species Pleurobranchidae 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
NPT137 Cell Line L1210 Mus musculus Activity = 550.0 Zone units PMID[470962]
NPT404 Cell Line CCRF-CEM Homo sapiens Activity = 550.0 Zone units PMID[470962]
NPT730 Cell Line MC-38 Mus musculus Activity = 550.0 Zone units PMID[470962]
NPT168 Cell Line P388 Mus musculus IC50 = 4.0 nM PMID[470963]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. GI50 = 5.754 nM PMID[470962]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. TGI = 128.82 nM PMID[470962]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. LC50 = 16595.87 nM PMID[470962]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Activity = 550.0 Zone units PMID[470962]

☑ 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 NPC92829 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
0.9712 High Similarity NPC122404
0.9619 High Similarity NPC24462
0.9417 High Similarity NPC168733
0.9314 High Similarity NPC259476
0.8545 High Similarity NPC7797
0.8246 Intermediate Similarity NPC216335
0.7928 Intermediate Similarity NPC42590
0.6833 Remote Similarity NPC328052
0.6723 Remote Similarity NPC475800
0.6667 Remote Similarity NPC106479
0.6612 Remote Similarity NPC474725
0.6557 Remote Similarity NPC46764
0.6535 Remote Similarity NPC323532
0.6518 Remote Similarity NPC100313
0.6504 Remote Similarity NPC12270
0.6471 Remote Similarity NPC474563
0.6429 Remote Similarity NPC194642
0.6404 Remote Similarity NPC199543
0.6396 Remote Similarity NPC259009
0.6393 Remote Similarity NPC140251
0.6393 Remote Similarity NPC307903
0.6372 Remote Similarity NPC470378
0.6372 Remote Similarity NPC149761
0.6372 Remote Similarity NPC261994
0.6372 Remote Similarity NPC80401
0.6364 Remote Similarity NPC471034
0.6364 Remote Similarity NPC190704
0.6348 Remote Similarity NPC302008
0.6348 Remote Similarity NPC191094
0.6348 Remote Similarity NPC280804
0.6316 Remote Similarity NPC314500
0.6316 Remote Similarity NPC299185
0.6316 Remote Similarity NPC476168
0.6293 Remote Similarity NPC138245
0.6293 Remote Similarity NPC84018
0.6293 Remote Similarity NPC231060
0.629 Remote Similarity NPC476290
0.6283 Remote Similarity NPC77001
0.6283 Remote Similarity NPC253618
0.6271 Remote Similarity NPC234542
0.6269 Remote Similarity NPC477352
0.6261 Remote Similarity NPC147272
0.6261 Remote Similarity NPC181594
0.6261 Remote Similarity NPC144739
0.626 Remote Similarity NPC128210
0.625 Remote Similarity NPC472495
0.625 Remote Similarity NPC153604
0.6239 Remote Similarity NPC46881
0.6228 Remote Similarity NPC232202
0.6226 Remote Similarity NPC474433
0.622 Remote Similarity NPC470540
0.6218 Remote Similarity NPC473224
0.6207 Remote Similarity NPC101233
0.6207 Remote Similarity NPC29247
0.6207 Remote Similarity NPC473314
0.6207 Remote Similarity NPC215271
0.6207 Remote Similarity NPC111524
0.6207 Remote Similarity NPC289539
0.6207 Remote Similarity NPC292374
0.6207 Remote Similarity NPC64006
0.6207 Remote Similarity NPC104371
0.6207 Remote Similarity NPC129004
0.6207 Remote Similarity NPC91772
0.6207 Remote Similarity NPC153775
0.6207 Remote Similarity NPC261333
0.6207 Remote Similarity NPC24861
0.6202 Remote Similarity NPC476956
0.6198 Remote Similarity NPC266
0.6194 Remote Similarity NPC478207
0.619 Remote Similarity NPC476269
0.6186 Remote Similarity NPC167380
0.6186 Remote Similarity NPC111187
0.6186 Remote Similarity NPC190080
0.6182 Remote Similarity NPC471036
0.6182 Remote Similarity NPC243347
0.6182 Remote Similarity NPC291320
0.6174 Remote Similarity NPC211403
0.6174 Remote Similarity NPC198054
0.6174 Remote Similarity NPC198242
0.6168 Remote Similarity NPC253703
0.6168 Remote Similarity NPC314858
0.6168 Remote Similarity NPC200085
0.6168 Remote Similarity NPC51695
0.6167 Remote Similarity NPC39683
0.6161 Remote Similarity NPC472738
0.6161 Remote Similarity NPC472986
0.6161 Remote Similarity NPC472985
0.616 Remote Similarity NPC140409
0.616 Remote Similarity NPC11491
0.616 Remote Similarity NPC156248
0.6154 Remote Similarity NPC259042
0.6154 Remote Similarity NPC41070
0.6154 Remote Similarity NPC157686
0.6154 Remote Similarity NPC472485
0.6142 Remote Similarity NPC89018
0.6134 Remote Similarity NPC471038
0.6131 Remote Similarity NPC96425
0.6126 Remote Similarity NPC97505
0.6121 Remote Similarity NPC59170
0.6121 Remote Similarity NPC472496
0.6121 Remote Similarity NPC226513
0.6116 Remote Similarity NPC164551
0.6111 Remote Similarity NPC170294
0.6106 Remote Similarity NPC165895
0.6106 Remote Similarity NPC472497
0.6106 Remote Similarity NPC298904
0.6102 Remote Similarity NPC134072
0.6102 Remote Similarity NPC234993
0.6102 Remote Similarity NPC140242
0.6102 Remote Similarity NPC242848
0.6102 Remote Similarity NPC264979
0.6102 Remote Similarity NPC135548
0.6098 Remote Similarity NPC166607
0.6098 Remote Similarity NPC37600
0.6095 Remote Similarity NPC102313
0.6095 Remote Similarity NPC199316
0.6094 Remote Similarity NPC88867
0.6094 Remote Similarity NPC226608
0.6091 Remote Similarity NPC145143
0.6091 Remote Similarity NPC110780
0.6087 Remote Similarity NPC180849
0.6087 Remote Similarity NPC46758
0.6087 Remote Similarity NPC153853
0.6083 Remote Similarity NPC110897
0.6083 Remote Similarity NPC41971
0.6083 Remote Similarity NPC127408
0.6083 Remote Similarity NPC180733
0.6083 Remote Similarity NPC291785
0.6083 Remote Similarity NPC477655
0.6083 Remote Similarity NPC154072
0.6083 Remote Similarity NPC470388
0.6083 Remote Similarity NPC37047
0.608 Remote Similarity NPC475191
0.608 Remote Similarity NPC322912
0.6071 Remote Similarity NPC102292
0.6071 Remote Similarity NPC292553
0.6068 Remote Similarity NPC470386
0.6068 Remote Similarity NPC469982
0.6068 Remote Similarity NPC470385
0.6068 Remote Similarity NPC148000
0.6068 Remote Similarity NPC469596
0.6068 Remote Similarity NPC225474
0.6068 Remote Similarity NPC47853
0.6066 Remote Similarity NPC469985
0.6055 Remote Similarity NPC148685
0.6055 Remote Similarity NPC164999
0.6055 Remote Similarity NPC157895
0.6055 Remote Similarity NPC104120
0.6053 Remote Similarity NPC16377
0.605 Remote Similarity NPC170978
0.605 Remote Similarity NPC474395
0.605 Remote Similarity NPC253586
0.605 Remote Similarity NPC473963
0.6048 Remote Similarity NPC471246
0.6048 Remote Similarity NPC78966
0.6048 Remote Similarity NPC284732
0.6048 Remote Similarity NPC216636
0.6047 Remote Similarity NPC470466
0.6036 Remote Similarity NPC472498
0.6036 Remote Similarity NPC105173
0.6036 Remote Similarity NPC312480
0.6034 Remote Similarity NPC73457
0.6034 Remote Similarity NPC278106
0.6033 Remote Similarity NPC46848
0.6033 Remote Similarity NPC14634
0.6033 Remote Similarity NPC121218
0.6033 Remote Similarity NPC253886
0.6033 Remote Similarity NPC308824
0.6033 Remote Similarity NPC242666
0.6033 Remote Similarity NPC111292
0.6033 Remote Similarity NPC75941
0.6029 Remote Similarity NPC476957
0.6019 Remote Similarity NPC269543
0.6019 Remote Similarity NPC247783
0.6018 Remote Similarity NPC473226
0.6018 Remote Similarity NPC187545
0.6018 Remote Similarity NPC153699
0.6018 Remote Similarity NPC470955
0.6018 Remote Similarity NPC185638
0.6018 Remote Similarity NPC76164
0.6017 Remote Similarity NPC266899
0.6017 Remote Similarity NPC470232
0.6017 Remote Similarity NPC288906
0.6017 Remote Similarity NPC29112
0.6017 Remote Similarity NPC98639
0.6017 Remote Similarity NPC263135
0.6017 Remote Similarity NPC271195
0.6017 Remote Similarity NPC272617
0.6016 Remote Similarity NPC160843
0.6016 Remote Similarity NPC474281
0.6016 Remote Similarity NPC14537
0.6 Remote Similarity NPC472970
0.6 Remote Similarity NPC469319
0.6 Remote Similarity NPC476190
0.6 Remote Similarity NPC57954
0.6 Remote Similarity NPC174663
0.6 Remote Similarity NPC14151
0.6 Remote Similarity NPC78427
0.6 Remote Similarity NPC213832
0.6 Remote Similarity NPC37628

  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 NPC92829 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
0.6504 Remote Similarity NPD1719 Phase 1
0.6111 Remote Similarity NPD5215 Approved
0.6099 Remote Similarity NPD6334 Approved
0.6099 Remote Similarity NPD6333 Approved
0.6031 Remote Similarity NPD4522 Approved
0.5969 Remote Similarity NPD5167 Approved
0.595 Remote Similarity NPD8418 Phase 2
0.5906 Remote Similarity NPD6420 Discontinued
0.5906 Remote Similarity NPD5169 Approved
0.5877 Remote Similarity NPD3618 Phase 1
0.5873 Remote Similarity NPD5168 Approved
0.5859 Remote Similarity NPD5127 Approved
0.5859 Remote Similarity NPD5216 Approved
0.5859 Remote Similarity NPD5217 Approved
0.584 Remote Similarity NPD7333 Discontinued
0.5827 Remote Similarity NPD6914 Discontinued
0.5804 Remote Similarity NPD3667 Approved
0.5789 Remote Similarity NPD7100 Approved
0.5789 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5763 Remote Similarity NPD8034 Phase 2
0.5763 Remote Similarity NPD8035 Phase 2
0.5702 Remote Similarity NPD4786 Approved
0.5683 Remote Similarity NPD6033 Approved
0.5625 Remote Similarity NPD5128 Approved
0.561 Remote Similarity NPD4225 Approved
0.5603 Remote Similarity NPD5956 Approved
0.56 Remote Similarity NPD3653 Clinical (unspecified phase)
0.56 Remote Similarity NPD5211 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