Structure

Physi-Chem Properties

Molecular Weight:  482.39
Volume:  533.614
LogP:  4.694
LogD:  5.798
LogS:  -6.126
# Rotatable Bonds:  4
TPSA:  49.54
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.295
Synthetic Accessibility Score:  5.351
Fsp3:  0.839
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.785
MDCK Permeability:  1.0744261089712381e-05
Pgp-inhibitor:  0.973
Pgp-substrate:  0.24
Human Intestinal Absorption (HIA):  0.027
20% Bioavailability (F20%):  0.421
30% Bioavailability (F30%):  0.269

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.006
Plasma Protein Binding (PPB):  93.87875366210938%
Volume Distribution (VD):  0.587
Pgp-substrate:  1.9296523332595825%

ADMET: Metabolism

CYP1A2-inhibitor:  0.037
CYP1A2-substrate:  0.223
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.931
CYP2C9-inhibitor:  0.103
CYP2C9-substrate:  0.088
CYP2D6-inhibitor:  0.646
CYP2D6-substrate:  0.688
CYP3A4-inhibitor:  0.803
CYP3A4-substrate:  0.869

ADMET: Excretion

Clearance (CL):  4.867
Half-life (T1/2):  0.127

ADMET: Toxicity

hERG Blockers:  0.217
Human Hepatotoxicity (H-HT):  0.398
Drug-inuced Liver Injury (DILI):  0.099
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.254
Maximum Recommended Daily Dose:  0.296
Skin Sensitization:  0.541
Carcinogencity:  0.006
Eye Corrosion:  0.013
Eye Irritation:  0.057
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC56796

Natural Product ID:  NPC56796
Common Name*:   Plakinamine E
IUPAC Name:   (3S,4R,5R,9R,10R,13R,14R,17R)-3-(dimethylamino)-10,13-dimethyl-17-[(2R)-1-(1-oxido-4-propan-2-ylidene-2,3-dihydropyrrol-1-ium-5-yl)propan-2-yl]-2,3,4,5,6,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-4-ol
Synonyms:   Plakinamine E
Standard InCHIKey:  QUWDXZBGZWUKTR-CWNRNWKTSA-N
Standard InCHI:  InChI=1S/C31H50N2O2/c1-19(2)21-14-17-33(35)28(21)18-20(3)23-10-11-24-22-8-9-26-29(34)27(32(6)7)13-16-31(26,5)25(22)12-15-30(23,24)4/h8,20,23-27,29,34H,9-18H2,1-7H3/t20-,23-,24+,25+,26+,27+,29-,30-,31-/m1/s1
SMILES:  CC(=C1CCN(=C1C[C@@H](C)[C@H]1CC[C@H]2C3=CC[C@H]4[C@H]([C@H](CC[C@]4(C)[C@H]3CC[C@]12C)N(C)C)O)=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL486263
PubChem CID:   15907379
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

*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
NPO32899 corticium Genus Plakinidae Eukaryota n.a. n.a. n.a. PMID[11720539]

☑ 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
NPT111 Cell Line K562 Homo sapiens LC50 = 0.2 ug.mL-1 PMID[525187]
NPT20 Organism Candida albicans Candida albicans IZ = 12.0 mm PMID[525187]

☑ 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 NPC56796 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
0.9515 High Similarity NPC25340
0.9223 High Similarity NPC474583
0.8585 High Similarity NPC471083
0.8349 Intermediate Similarity NPC55462
0.8286 Intermediate Similarity NPC476903
0.8073 Intermediate Similarity NPC50815
0.8053 Intermediate Similarity NPC472359
0.7909 Intermediate Similarity NPC247060
0.7838 Intermediate Similarity NPC241879
0.7727 Intermediate Similarity NPC275686
0.7706 Intermediate Similarity NPC240650
0.7607 Intermediate Similarity NPC80834
0.7607 Intermediate Similarity NPC469968
0.7593 Intermediate Similarity NPC280710
0.7593 Intermediate Similarity NPC243985
0.7565 Intermediate Similarity NPC159367
0.7522 Intermediate Similarity NPC90538
0.7478 Intermediate Similarity NPC169375
0.7455 Intermediate Similarity NPC289140
0.7398 Intermediate Similarity NPC242692
0.7391 Intermediate Similarity NPC36497
0.7368 Intermediate Similarity NPC45365
0.7368 Intermediate Similarity NPC293299
0.7232 Intermediate Similarity NPC140300
0.7207 Intermediate Similarity NPC311164
0.7207 Intermediate Similarity NPC272732
0.72 Intermediate Similarity NPC472458
0.7179 Intermediate Similarity NPC46981
0.717 Intermediate Similarity NPC75810
0.7168 Intermediate Similarity NPC91604
0.7168 Intermediate Similarity NPC140685
0.7131 Intermediate Similarity NPC165396
0.713 Intermediate Similarity NPC34754
0.7083 Intermediate Similarity NPC474459
0.7083 Intermediate Similarity NPC66862
0.7025 Intermediate Similarity NPC474452
0.7009 Intermediate Similarity NPC119329
0.7009 Intermediate Similarity NPC152684
0.7 Intermediate Similarity NPC72753
0.7 Intermediate Similarity NPC472313
0.7 Intermediate Similarity NPC328052
0.6967 Remote Similarity NPC478137
0.6957 Remote Similarity NPC135799
0.6949 Remote Similarity NPC86906
0.6944 Remote Similarity NPC166458
0.693 Remote Similarity NPC474164
0.6899 Remote Similarity NPC237286
0.6897 Remote Similarity NPC118275
0.6864 Remote Similarity NPC475239
0.6864 Remote Similarity NPC212874
0.6838 Remote Similarity NPC176012
0.6814 Remote Similarity NPC473314
0.6807 Remote Similarity NPC258130
0.6726 Remote Similarity NPC93027
0.6723 Remote Similarity NPC470596
0.6695 Remote Similarity NPC152718
0.6667 Remote Similarity NPC477292
0.6667 Remote Similarity NPC79238
0.6642 Remote Similarity NPC132847
0.6638 Remote Similarity NPC167419
0.6636 Remote Similarity NPC257962
0.6635 Remote Similarity NPC189883
0.6604 Remote Similarity NPC1319
0.6587 Remote Similarity NPC28280
0.6587 Remote Similarity NPC304646
0.6571 Remote Similarity NPC214570
0.6557 Remote Similarity NPC470595
0.6555 Remote Similarity NPC226509
0.6555 Remote Similarity NPC476755
0.6549 Remote Similarity NPC84171
0.6545 Remote Similarity NPC24733
0.6542 Remote Similarity NPC236112
0.6538 Remote Similarity NPC141071
0.6538 Remote Similarity NPC257347
0.6538 Remote Similarity NPC471723
0.6514 Remote Similarity NPC246956
0.6509 Remote Similarity NPC138621
0.6509 Remote Similarity NPC275910
0.6509 Remote Similarity NPC6978
0.6509 Remote Similarity NPC167037
0.6509 Remote Similarity NPC244385
0.6509 Remote Similarity NPC285761
0.6508 Remote Similarity NPC470540
0.6504 Remote Similarity NPC85001
0.6504 Remote Similarity NPC253645
0.6504 Remote Similarity NPC147835
0.6504 Remote Similarity NPC95920
0.65 Remote Similarity NPC98765
0.6496 Remote Similarity NPC292819
0.6496 Remote Similarity NPC4834
0.6481 Remote Similarity NPC474531
0.6481 Remote Similarity NPC192456
0.6481 Remote Similarity NPC109533
0.6476 Remote Similarity NPC321016
0.6476 Remote Similarity NPC107059
0.6476 Remote Similarity NPC46160
0.6476 Remote Similarity NPC237460
0.6476 Remote Similarity NPC129165
0.6476 Remote Similarity NPC202642
0.6476 Remote Similarity NPC134330
0.6476 Remote Similarity NPC73875
0.6476 Remote Similarity NPC321381
0.6476 Remote Similarity NPC240604
0.6476 Remote Similarity NPC300324
0.6449 Remote Similarity NPC80530
0.6449 Remote Similarity NPC209430
0.6449 Remote Similarity NPC30986
0.6449 Remote Similarity NPC273410
0.6446 Remote Similarity NPC469958
0.6442 Remote Similarity NPC476904
0.6422 Remote Similarity NPC470049
0.6422 Remote Similarity NPC30166
0.6422 Remote Similarity NPC283277
0.6422 Remote Similarity NPC224072
0.6422 Remote Similarity NPC39966
0.6415 Remote Similarity NPC318495
0.6415 Remote Similarity NPC198968
0.6415 Remote Similarity NPC155986
0.6412 Remote Similarity NPC478138
0.6408 Remote Similarity NPC21773
0.6393 Remote Similarity NPC195841
0.6393 Remote Similarity NPC233256
0.6389 Remote Similarity NPC236237
0.6389 Remote Similarity NPC322313
0.6389 Remote Similarity NPC13554
0.6389 Remote Similarity NPC102253
0.6381 Remote Similarity NPC288035
0.6381 Remote Similarity NPC304309
0.6381 Remote Similarity NPC134847
0.6381 Remote Similarity NPC22105
0.6381 Remote Similarity NPC162742
0.6381 Remote Similarity NPC136188
0.6381 Remote Similarity NPC118508
0.6381 Remote Similarity NPC28657
0.6381 Remote Similarity NPC121744
0.6381 Remote Similarity NPC230301
0.6381 Remote Similarity NPC322353
0.6381 Remote Similarity NPC285893
0.6372 Remote Similarity NPC324405
0.6355 Remote Similarity NPC302041
0.6355 Remote Similarity NPC87604
0.6355 Remote Similarity NPC205455
0.6355 Remote Similarity NPC473943
0.6355 Remote Similarity NPC477514
0.6355 Remote Similarity NPC477522
0.6355 Remote Similarity NPC186191
0.6355 Remote Similarity NPC474216
0.6355 Remote Similarity NPC85346
0.6355 Remote Similarity NPC65897
0.6349 Remote Similarity NPC476498
0.6349 Remote Similarity NPC124358
0.6346 Remote Similarity NPC474140
0.633 Remote Similarity NPC470383
0.6321 Remote Similarity NPC247325
0.6321 Remote Similarity NPC470362
0.6321 Remote Similarity NPC7214
0.6321 Remote Similarity NPC244488
0.6321 Remote Similarity NPC113733
0.632 Remote Similarity NPC287764
0.6308 Remote Similarity NPC35037
0.6306 Remote Similarity NPC478102
0.6306 Remote Similarity NPC470077
0.6306 Remote Similarity NPC209802
0.6306 Remote Similarity NPC124172
0.6296 Remote Similarity NPC328714
0.6296 Remote Similarity NPC81306
0.6296 Remote Similarity NPC109546
0.6296 Remote Similarity NPC84694
0.6296 Remote Similarity NPC28862
0.6296 Remote Similarity NPC143182
0.6296 Remote Similarity NPC47982
0.6288 Remote Similarity NPC469943
0.6273 Remote Similarity NPC202389
0.6273 Remote Similarity NPC20853
0.6273 Remote Similarity NPC218616
0.6273 Remote Similarity NPC215474
0.6273 Remote Similarity NPC248886
0.6273 Remote Similarity NPC49964
0.6273 Remote Similarity NPC201852
0.6273 Remote Similarity NPC296701
0.6273 Remote Similarity NPC87489
0.6273 Remote Similarity NPC101462
0.6262 Remote Similarity NPC34019
0.626 Remote Similarity NPC230677
0.625 Remote Similarity NPC318390
0.625 Remote Similarity NPC476499
0.6239 Remote Similarity NPC241290
0.6239 Remote Similarity NPC26117
0.6239 Remote Similarity NPC209944
0.6239 Remote Similarity NPC234193
0.6239 Remote Similarity NPC164840
0.623 Remote Similarity NPC473254
0.623 Remote Similarity NPC474563
0.622 Remote Similarity NPC477291
0.6218 Remote Similarity NPC184033
0.6216 Remote Similarity NPC317458
0.6216 Remote Similarity NPC477818
0.6216 Remote Similarity NPC110778
0.6216 Remote Similarity NPC207013
0.6216 Remote Similarity NPC113978

  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 NPC56796 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
0.7117 Intermediate Similarity NPD5771 Approved
0.6818 Remote Similarity NPD4722 Approved
0.6818 Remote Similarity NPD4723 Approved
0.6389 Remote Similarity NPD7525 Registered
0.6381 Remote Similarity NPD7339 Approved
0.6381 Remote Similarity NPD6942 Approved
0.6311 Remote Similarity NPD6939 Phase 2
0.6311 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6299 Remote Similarity NPD8298 Phase 2
0.6239 Remote Similarity NPD5707 Approved
0.6202 Remote Similarity NPD7755 Approved
0.6202 Remote Similarity NPD7754 Approved
0.6183 Remote Similarity NPD7522 Discontinued
0.6168 Remote Similarity NPD3701 Clinical (unspecified phase)
0.6121 Remote Similarity NPD4001 Clinical (unspecified phase)
0.6117 Remote Similarity NPD6705 Phase 1
0.6116 Remote Similarity NPD8418 Phase 2
0.6102 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6094 Remote Similarity NPD7336 Phase 2
0.6094 Remote Similarity NPD7335 Phase 2
0.6094 Remote Similarity NPD7337 Clinical (unspecified phase)
0.6063 Remote Similarity NPD6420 Discontinued
0.6034 Remote Similarity NPD5328 Approved
0.6018 Remote Similarity NPD4786 Approved
0.6 Remote Similarity NPD7645 Phase 2
0.5981 Remote Similarity NPD6926 Approved
0.5981 Remote Similarity NPD6924 Approved
0.597 Remote Similarity NPD6908 Approved
0.597 Remote Similarity NPD6909 Approved
0.595 Remote Similarity NPD7919 Phase 3
0.595 Remote Similarity NPD7920 Phase 3
0.5943 Remote Similarity NPD4243 Approved
0.5932 Remote Similarity NPD6079 Approved
0.5913 Remote Similarity NPD3618 Phase 1
0.5902 Remote Similarity NPD8088 Phase 1
0.5882 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5873 Remote Similarity NPD7333 Discontinued
0.5873 Remote Similarity NPD6920 Discontinued
0.5872 Remote Similarity NPD6933 Approved
0.5854 Remote Similarity NPD6404 Discontinued
0.5841 Remote Similarity NPD3667 Approved
0.5833 Remote Similarity NPD4785 Approved
0.5833 Remote Similarity NPD4784 Approved
0.5827 Remote Similarity NPD7646 Clinical (unspecified phase)
0.5793 Remote Similarity NPD6333 Approved
0.5793 Remote Similarity NPD6334 Approved
0.5781 Remote Similarity NPD6415 Discontinued
0.5755 Remote Similarity NPD6923 Approved
0.5755 Remote Similarity NPD6922 Approved
0.575 Remote Similarity NPD4202 Approved
0.5745 Remote Similarity NPD6914 Discontinued
0.5739 Remote Similarity NPD3666 Approved
0.5739 Remote Similarity NPD3665 Phase 1
0.5739 Remote Similarity NPD3133 Approved
0.5738 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5727 Remote Similarity NPD1346 Approved
0.5726 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5725 Remote Similarity NPD8077 Approved
0.5725 Remote Similarity NPD8078 Approved
0.5714 Remote Similarity NPD6701 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6700 Approved
0.5714 Remote Similarity NPD6929 Approved
0.5701 Remote Similarity NPD7144 Approved
0.5701 Remote Similarity NPD7143 Approved
0.5664 Remote Similarity NPD7509 Discontinued
0.5664 Remote Similarity NPD6931 Approved
0.5664 Remote Similarity NPD6930 Phase 2
0.5664 Remote Similarity NPD4748 Discontinued
0.5659 Remote Similarity NPD8174 Phase 2
0.5648 Remote Similarity NPD7151 Approved
0.5648 Remote Similarity NPD7152 Approved
0.5648 Remote Similarity NPD7150 Approved
0.5636 Remote Similarity NPD4190 Phase 3
0.5636 Remote Similarity NPD5275 Approved
0.5625 Remote Similarity NPD6640 Phase 3
0.5625 Remote Similarity NPD5357 Phase 1
0.561 Remote Similarity NPD5222 Approved
0.561 Remote Similarity NPD4697 Phase 3
0.561 Remote Similarity NPD5220 Clinical (unspecified phase)
0.561 Remote Similarity NPD5221 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