Structure

Physi-Chem Properties

Molecular Weight:  387.24
Volume:  413.67
LogP:  4.606
LogD:  3.735
LogS:  -3.6
# Rotatable Bonds:  4
TPSA:  82.69
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.531
Synthetic Accessibility Score:  4.961
Fsp3:  0.609
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.91
MDCK Permeability:  1.0463113540026825e-05
Pgp-inhibitor:  0.03
Pgp-substrate:  0.894
Human Intestinal Absorption (HIA):  0.373
20% Bioavailability (F20%):  0.024
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.038
Plasma Protein Binding (PPB):  99.05457305908203%
Volume Distribution (VD):  1.016
Pgp-substrate:  2.3436336517333984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.744
CYP1A2-substrate:  0.801
CYP2C19-inhibitor:  0.277
CYP2C19-substrate:  0.682
CYP2C9-inhibitor:  0.699
CYP2C9-substrate:  0.757
CYP2D6-inhibitor:  0.413
CYP2D6-substrate:  0.331
CYP3A4-inhibitor:  0.691
CYP3A4-substrate:  0.302

ADMET: Excretion

Clearance (CL):  3.95
Half-life (T1/2):  0.487

ADMET: Toxicity

hERG Blockers:  0.006
Human Hepatotoxicity (H-HT):  0.347
Drug-inuced Liver Injury (DILI):  0.377
AMES Toxicity:  0.076
Rat Oral Acute Toxicity:  0.422
Maximum Recommended Daily Dose:  0.406
Skin Sensitization:  0.325
Carcinogencity:  0.041
Eye Corrosion:  0.003
Eye Irritation:  0.026
Respiratory Toxicity:  0.88

Download Data

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

  Natural Product: NPC476328

Natural Product ID:  NPC476328
Common Name*:   JKLSVNLLSFWULH-ZPIPSWCUSA-N
IUPAC Name:   n.a.
Synonyms:   CJ-21058
Standard InCHIKey:  JKLSVNLLSFWULH-ZPIPSWCUSA-N
Standard InCHI:  InChI=1S/C23H33NO4/c1-6-7-16-14(3)11-15-9-8-13(2)10-17(15)23(16,4)21(27)19-20(26)18(12-25)24(5)22(19)28/h6-7,11,13,15-18,25-26H,8-10,12H2,1-5H3/b7-6+/t13-,15+,16-,17+,18?,23-/m1/s1
SMILES:  C/C=C/[C@@H]1C(=C[C@H]2[C@@H]([C@]1(C)C(=O)C1=C(O)C(N(C1=O)C)CO)C[C@@H](CC2)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL565009
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000091] Pyrrolines

*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
NPO33463 geomyces pannorum Species n.a. Eukaryota n.a. n.a. n.a. PMID[19102658]

☑ 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 = 12000.0 nM PMID[529755]

☑ 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 NPC476328 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
0.9798 High Similarity NPC476276
0.8095 Intermediate Similarity NPC77703
0.7818 Intermediate Similarity NPC476918
0.7664 Intermediate Similarity NPC477964
0.7636 Intermediate Similarity NPC476926
0.7545 Intermediate Similarity NPC476921
0.7282 Intermediate Similarity NPC324506
0.7193 Intermediate Similarity NPC476920
0.7043 Intermediate Similarity NPC476919
0.6964 Remote Similarity NPC474001
0.6942 Remote Similarity NPC474006
0.6923 Remote Similarity NPC76283
0.6923 Remote Similarity NPC476290
0.6916 Remote Similarity NPC17143
0.6916 Remote Similarity NPC47230
0.6897 Remote Similarity NPC140251
0.6897 Remote Similarity NPC307903
0.687 Remote Similarity NPC185929
0.6847 Remote Similarity NPC184033
0.6842 Remote Similarity NPC474563
0.6833 Remote Similarity NPC145501
0.6814 Remote Similarity NPC34193
0.6814 Remote Similarity NPC476922
0.6807 Remote Similarity NPC476269
0.6789 Remote Similarity NPC247316
0.6783 Remote Similarity NPC475239
0.678 Remote Similarity NPC63511
0.6762 Remote Similarity NPC182106
0.6762 Remote Similarity NPC311769
0.6754 Remote Similarity NPC226509
0.6754 Remote Similarity NPC152718
0.6752 Remote Similarity NPC24596
0.6721 Remote Similarity NPC477121
0.6698 Remote Similarity NPC322672
0.6698 Remote Similarity NPC157479
0.6667 Remote Similarity NPC314550
0.6638 Remote Similarity NPC469958
0.6636 Remote Similarity NPC473525
0.6635 Remote Similarity NPC215474
0.661 Remote Similarity NPC207820
0.6607 Remote Similarity NPC247220
0.6606 Remote Similarity NPC473056
0.6604 Remote Similarity NPC319913
0.6604 Remote Similarity NPC147513
0.6585 Remote Similarity NPC476190
0.6574 Remote Similarity NPC259252
0.6525 Remote Similarity NPC475800
0.6504 Remote Similarity NPC288629
0.6486 Remote Similarity NPC93027
0.6475 Remote Similarity NPC469597
0.6471 Remote Similarity NPC474099
0.6449 Remote Similarity NPC472931
0.6449 Remote Similarity NPC472940
0.6446 Remote Similarity NPC474431
0.6446 Remote Similarity NPC474411
0.6442 Remote Similarity NPC2482
0.6435 Remote Similarity NPC316730
0.6429 Remote Similarity NPC476754
0.6417 Remote Similarity NPC474725
0.641 Remote Similarity NPC474828
0.641 Remote Similarity NPC474827
0.641 Remote Similarity NPC68001
0.641 Remote Similarity NPC199831
0.6408 Remote Similarity NPC82635
0.64 Remote Similarity NPC471673
0.6389 Remote Similarity NPC118648
0.6389 Remote Similarity NPC475022
0.6389 Remote Similarity NPC222613
0.6385 Remote Similarity NPC96010
0.6385 Remote Similarity NPC317654
0.6381 Remote Similarity NPC99308
0.6373 Remote Similarity NPC1254
0.6364 Remote Similarity NPC97614
0.6364 Remote Similarity NPC31985
0.6364 Remote Similarity NPC72688
0.6364 Remote Similarity NPC1015
0.6364 Remote Similarity NPC328052
0.6357 Remote Similarity NPC321197
0.6356 Remote Similarity NPC470073
0.6356 Remote Similarity NPC470596
0.6348 Remote Similarity NPC140685
0.633 Remote Similarity NPC58063
0.6325 Remote Similarity NPC476755
0.6325 Remote Similarity NPC58200
0.6321 Remote Similarity NPC473810
0.6303 Remote Similarity NPC230677
0.6296 Remote Similarity NPC469948
0.629 Remote Similarity NPC176336
0.6281 Remote Similarity NPC274895
0.6281 Remote Similarity NPC218602
0.6281 Remote Similarity NPC175585
0.6271 Remote Similarity NPC318544
0.6271 Remote Similarity NPC98765
0.627 Remote Similarity NPC471109
0.6262 Remote Similarity NPC41539
0.6262 Remote Similarity NPC21667
0.6261 Remote Similarity NPC140300
0.626 Remote Similarity NPC7797
0.625 Remote Similarity NPC176773
0.6239 Remote Similarity NPC474732
0.6239 Remote Similarity NPC474733
0.6239 Remote Similarity NPC145879
0.6239 Remote Similarity NPC94666
0.6239 Remote Similarity NPC474778
0.6239 Remote Similarity NPC31564
0.623 Remote Similarity NPC469603
0.6226 Remote Similarity NPC44963
0.6226 Remote Similarity NPC472684
0.6226 Remote Similarity NPC116797
0.6226 Remote Similarity NPC189237
0.6226 Remote Similarity NPC121984
0.6226 Remote Similarity NPC90150
0.6216 Remote Similarity NPC249312
0.621 Remote Similarity NPC478137
0.6204 Remote Similarity NPC473246
0.6204 Remote Similarity NPC85774
0.6204 Remote Similarity NPC214043
0.62 Remote Similarity NPC328895
0.6198 Remote Similarity NPC470595
0.6195 Remote Similarity NPC242069
0.6195 Remote Similarity NPC476753
0.6195 Remote Similarity NPC476752
0.6186 Remote Similarity NPC474244
0.6186 Remote Similarity NPC247060
0.6186 Remote Similarity NPC50815
0.6186 Remote Similarity NPC469598
0.6183 Remote Similarity NPC309525
0.6182 Remote Similarity NPC93778
0.6182 Remote Similarity NPC475740
0.6179 Remote Similarity NPC143173
0.6174 Remote Similarity NPC476903
0.6174 Remote Similarity NPC472733
0.6174 Remote Similarity NPC472734
0.6168 Remote Similarity NPC311092
0.6168 Remote Similarity NPC103486
0.6154 Remote Similarity NPC325946
0.6147 Remote Similarity NPC255174
0.6147 Remote Similarity NPC33881
0.614 Remote Similarity NPC473162
0.614 Remote Similarity NPC474690
0.614 Remote Similarity NPC473172
0.6132 Remote Similarity NPC472478
0.6126 Remote Similarity NPC471722
0.6126 Remote Similarity NPC292491
0.6126 Remote Similarity NPC34754
0.6126 Remote Similarity NPC310752
0.6121 Remote Similarity NPC472731
0.6121 Remote Similarity NPC52820
0.6121 Remote Similarity NPC472732
0.6121 Remote Similarity NPC208094
0.6117 Remote Similarity NPC473171
0.6116 Remote Similarity NPC169375
0.61 Remote Similarity NPC256846
0.6095 Remote Similarity NPC471409
0.6095 Remote Similarity NPC275494
0.6091 Remote Similarity NPC194417
0.6087 Remote Similarity NPC473170
0.6087 Remote Similarity NPC472932
0.6087 Remote Similarity NPC295347
0.6075 Remote Similarity NPC475863
0.6075 Remote Similarity NPC4166
0.6075 Remote Similarity NPC55869
0.6075 Remote Similarity NPC470034
0.6074 Remote Similarity NPC472413
0.6071 Remote Similarity NPC5509
0.6071 Remote Similarity NPC477943
0.6071 Remote Similarity NPC26959
0.6071 Remote Similarity NPC310010
0.6071 Remote Similarity NPC326627
0.6071 Remote Similarity NPC186688
0.6071 Remote Similarity NPC268406
0.6071 Remote Similarity NPC477973
0.6068 Remote Similarity NPC153776
0.6068 Remote Similarity NPC472729
0.6068 Remote Similarity NPC177680
0.6068 Remote Similarity NPC472730
0.6068 Remote Similarity NPC91604
0.6063 Remote Similarity NPC216335
0.6058 Remote Similarity NPC470525
0.6058 Remote Similarity NPC263582
0.6058 Remote Similarity NPC180886
0.6055 Remote Similarity NPC221758
0.6055 Remote Similarity NPC161423
0.6055 Remote Similarity NPC321187
0.6055 Remote Similarity NPC237712
0.6055 Remote Similarity NPC59453
0.6055 Remote Similarity NPC58841
0.6055 Remote Similarity NPC329043
0.6055 Remote Similarity NPC227064
0.6053 Remote Similarity NPC474736
0.6053 Remote Similarity NPC474807
0.6053 Remote Similarity NPC472930
0.6053 Remote Similarity NPC469939
0.6048 Remote Similarity NPC44733
0.6047 Remote Similarity NPC477143
0.6047 Remote Similarity NPC477140
0.6038 Remote Similarity NPC27817
0.6038 Remote Similarity NPC472490
0.6036 Remote Similarity NPC470523
0.6036 Remote Similarity NPC90652

  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 NPC476328 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
0.687 Remote Similarity NPD7333 Discontinued
0.6316 Remote Similarity NPD5349 Clinical (unspecified phase)
0.625 Remote Similarity NPD6909 Approved
0.625 Remote Similarity NPD6908 Approved
0.621 Remote Similarity NPD1376 Discontinued
0.6071 Remote Similarity NPD4753 Phase 2
0.6055 Remote Similarity NPD3665 Phase 1
0.6055 Remote Similarity NPD4786 Approved
0.6055 Remote Similarity NPD3133 Approved
0.6055 Remote Similarity NPD3666 Approved
0.6019 Remote Similarity NPD3667 Approved
0.6 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6 Remote Similarity NPD6914 Discontinued
0.5981 Remote Similarity NPD4695 Discontinued
0.5965 Remote Similarity NPD6079 Approved
0.5963 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5948 Remote Similarity NPD5210 Approved
0.5948 Remote Similarity NPD4629 Approved
0.5946 Remote Similarity NPD3618 Phase 1
0.5941 Remote Similarity NPD4137 Phase 3
0.5929 Remote Similarity NPD5328 Approved
0.5882 Remote Similarity NPD4691 Approved
0.5882 Remote Similarity NPD7751 Phase 1
0.5882 Remote Similarity NPD4747 Approved
0.5865 Remote Similarity NPD4058 Approved
0.5865 Remote Similarity NPD5733 Approved
0.5865 Remote Similarity NPD4687 Approved
0.5852 Remote Similarity NPD6792 Phase 3
0.5847 Remote Similarity NPD6083 Phase 2
0.5847 Remote Similarity NPD6084 Phase 2
0.5846 Remote Similarity NPD7518 Approved
0.5846 Remote Similarity NPD7519 Approved
0.5846 Remote Similarity NPD7517 Approved
0.5833 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5826 Remote Similarity NPD7515 Phase 2
0.5804 Remote Similarity NPD5279 Phase 3
0.5789 Remote Similarity NPD7122 Discontinued
0.5769 Remote Similarity NPD7641 Discontinued
0.5763 Remote Similarity NPD5221 Approved
0.5763 Remote Similarity NPD5220 Clinical (unspecified phase)
0.5763 Remote Similarity NPD5222 Approved
0.575 Remote Similarity NPD5285 Approved
0.575 Remote Similarity NPD5286 Approved
0.575 Remote Similarity NPD4696 Approved
0.5727 Remote Similarity NPD4221 Approved
0.5727 Remote Similarity NPD4223 Phase 3
0.5725 Remote Similarity NPD7260 Phase 2
0.5714 Remote Similarity NPD8415 Approved
0.5714 Remote Similarity NPD4755 Approved
0.5714 Remote Similarity NPD5173 Approved
0.5714 Remote Similarity NPD5329 Approved
0.5714 Remote Similarity NPD6420 Discontinued
0.5705 Remote Similarity NPD8165 Discontinued
0.5682 Remote Similarity NPD6343 Approved
0.5682 Remote Similarity NPD7299 Clinical (unspecified phase)
0.5682 Remote Similarity NPD6345 Approved
0.5678 Remote Similarity NPD5695 Phase 3
0.5673 Remote Similarity NPD5276 Approved
0.5664 Remote Similarity NPD4519 Discontinued
0.5664 Remote Similarity NPD4623 Approved
0.5664 Remote Similarity NPD5690 Phase 2
0.5656 Remote Similarity NPD5211 Phase 2
0.5656 Remote Similarity NPD5224 Approved
0.5656 Remote Similarity NPD5225 Approved
0.5656 Remote Similarity NPD4633 Approved
0.5656 Remote Similarity NPD5226 Approved
0.5652 Remote Similarity NPD7285 Clinical (unspecified phase)
0.5648 Remote Similarity NPD3617 Approved
0.5641 Remote Similarity NPD6399 Phase 3
0.5641 Remote Similarity NPD4202 Approved
0.5636 Remote Similarity NPD8028 Phase 2
0.563 Remote Similarity NPD4697 Phase 3
0.5625 Remote Similarity NPD4197 Approved
0.5625 Remote Similarity NPD3668 Phase 3
0.562 Remote Similarity NPD2634 Clinical (unspecified phase)
0.562 Remote Similarity NPD4700 Approved
0.561 Remote Similarity NPD5175 Approved
0.561 Remote Similarity NPD5174 Approved
0.5603 Remote Similarity NPD4096 Approved
0.5603 Remote Similarity NPD790 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