Structure

Physi-Chem Properties

Molecular Weight:  436.35
Volume:  487.596
LogP:  6.39
LogD:  5.497
LogS:  -6.622
# Rotatable Bonds:  3
TPSA:  62.04
# H-Bond Aceptor:  3
# H-Bond Donor:  4
# Rings:  5
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.44
Synthetic Accessibility Score:  4.961
Fsp3:  0.724
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:  -5.076
MDCK Permeability:  1.9417644580244087e-05
Pgp-inhibitor:  0.436
Pgp-substrate:  0.975
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.969
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.104
Plasma Protein Binding (PPB):  98.12857818603516%
Volume Distribution (VD):  2.399
Pgp-substrate:  1.7504358291625977%

ADMET: Metabolism

CYP1A2-inhibitor:  0.242
CYP1A2-substrate:  0.434
CYP2C19-inhibitor:  0.161
CYP2C19-substrate:  0.457
CYP2C9-inhibitor:  0.314
CYP2C9-substrate:  0.493
CYP2D6-inhibitor:  0.751
CYP2D6-substrate:  0.912
CYP3A4-inhibitor:  0.908
CYP3A4-substrate:  0.359

ADMET: Excretion

Clearance (CL):  4.456
Half-life (T1/2):  0.077

ADMET: Toxicity

hERG Blockers:  0.816
Human Hepatotoxicity (H-HT):  0.631
Drug-inuced Liver Injury (DILI):  0.084
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.249
Maximum Recommended Daily Dose:  0.966
Skin Sensitization:  0.578
Carcinogencity:  0.044
Eye Corrosion:  0.005
Eye Irritation:  0.018
Respiratory Toxicity:  0.904

Download Data

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

  Natural Product: NPC167419

Natural Product ID:  NPC167419
Common Name*:   Plakinamine G
IUPAC Name:   (5Z)-5-[(2S)-2-[(3R,5S,9R,10S,13R,14R,17R)-3-amino-10,13-dimethyl-2,3,4,5,6,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]propylidene]-4-propan-2-ylpyrrol-2-one
Synonyms:   Plakinamine G
Standard InCHIKey:  CWLJITAGIPFLJD-UOJYZFCXSA-N
Standard InCHI:  InChI=1S/C29H44N2O/c1-17(2)22-16-27(32)31-26(22)14-18(3)23-8-9-24-21-7-6-19-15-20(30)10-12-28(19,4)25(21)11-13-29(23,24)5/h7,14,16-20,23-25H,6,8-13,15,30H2,1-5H3,(H,31,32)/b26-14-/t18-,19+,20-,23-,24+,25+,28+,29-/m1/s1
SMILES:  CC(C)C1=CC(=N/C/1=C[C@@H](C)[C@H]1CC[C@H]2C3=CC[C@H]4C[C@@H](CC[C@]4(C)[C@H]3CC[C@]12C)N)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL489759
PubChem CID:   21592303
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
NPO32780 corticium sp. Species Corticiaceae Eukaryota n.a. n.a. n.a. PMID[12193035]
NPO32780 corticium sp. Species Corticiaceae Eukaryota n.a. n.a. n.a. PMID[17391049]
NPO32780 corticium sp. Species Corticiaceae Eukaryota n.a. New Britain, Papua New Guinea n.a. PMID[24195491]
NPO32780 corticium sp. Species Corticiaceae Eukaryota n.a. n.a. n.a. PMID[7964780]

☑ 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
NPT76 Cell Line C6 Rattus norvegicus IC50 = 6.8 ug.mL-1 PMID[516834]

☑ 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 NPC167419 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
0.7979 Intermediate Similarity NPC152684
0.7849 Intermediate Similarity NPC283277
0.7708 Intermediate Similarity NPC166458
0.7604 Intermediate Similarity NPC24733
0.7553 Intermediate Similarity NPC257962
0.7477 Intermediate Similarity NPC230677
0.7292 Intermediate Similarity NPC472312
0.7273 Intermediate Similarity NPC175585
0.7188 Intermediate Similarity NPC329782
0.713 Intermediate Similarity NPC474583
0.7075 Intermediate Similarity NPC140685
0.7064 Intermediate Similarity NPC469958
0.7048 Intermediate Similarity NPC247220
0.701 Intermediate Similarity NPC118329
0.701 Intermediate Similarity NPC152039
0.6979 Remote Similarity NPC211322
0.6937 Remote Similarity NPC25340
0.6907 Remote Similarity NPC12035
0.6881 Remote Similarity NPC471083
0.6881 Remote Similarity NPC152718
0.6881 Remote Similarity NPC50815
0.6869 Remote Similarity NPC21667
0.6847 Remote Similarity NPC55462
0.6837 Remote Similarity NPC474122
0.6809 Remote Similarity NPC476904
0.6774 Remote Similarity NPC21773
0.6768 Remote Similarity NPC224072
0.6727 Remote Similarity NPC247060
0.6727 Remote Similarity NPC58200
0.6727 Remote Similarity NPC226509
0.6726 Remote Similarity NPC159367
0.6667 Remote Similarity NPC7214
0.6667 Remote Similarity NPC90538
0.6638 Remote Similarity NPC56796
0.66 Remote Similarity NPC215474
0.66 Remote Similarity NPC39966
0.6596 Remote Similarity NPC265789
0.6562 Remote Similarity NPC125828
0.6538 Remote Similarity NPC34754
0.6535 Remote Similarity NPC171639
0.6496 Remote Similarity NPC80834
0.6496 Remote Similarity NPC469968
0.6495 Remote Similarity NPC476308
0.6486 Remote Similarity NPC118275
0.6466 Remote Similarity NPC72753
0.6442 Remote Similarity NPC43308
0.6415 Remote Similarity NPC84171
0.6408 Remote Similarity NPC147513
0.6396 Remote Similarity NPC135799
0.6396 Remote Similarity NPC275686
0.6389 Remote Similarity NPC280710
0.6389 Remote Similarity NPC243985
0.6389 Remote Similarity NPC476754
0.6383 Remote Similarity NPC472831
0.6383 Remote Similarity NPC245223
0.6372 Remote Similarity NPC293299
0.6372 Remote Similarity NPC45365
0.6364 Remote Similarity NPC184033
0.6364 Remote Similarity NPC474164
0.6346 Remote Similarity NPC157479
0.6346 Remote Similarity NPC56107
0.6325 Remote Similarity NPC328052
0.6325 Remote Similarity NPC472359
0.6321 Remote Similarity NPC249312
0.6316 Remote Similarity NPC119329
0.6273 Remote Similarity NPC476903
0.6271 Remote Similarity NPC66862
0.627 Remote Similarity NPC237286
0.625 Remote Similarity NPC476329
0.6226 Remote Similarity NPC324405
0.6216 Remote Similarity NPC240650
0.6211 Remote Similarity NPC138409
0.6186 Remote Similarity NPC472313
0.6182 Remote Similarity NPC311164
0.6182 Remote Similarity NPC272732
0.6162 Remote Similarity NPC174803
0.6162 Remote Similarity NPC259989
0.6147 Remote Similarity NPC476752
0.6147 Remote Similarity NPC476753
0.614 Remote Similarity NPC176012
0.6121 Remote Similarity NPC36497
0.6095 Remote Similarity NPC75810
0.6091 Remote Similarity NPC473314
0.6087 Remote Similarity NPC98765
0.6083 Remote Similarity NPC474452
0.6071 Remote Similarity NPC4834
0.6068 Remote Similarity NPC169375
0.6063 Remote Similarity NPC109151
0.6048 Remote Similarity NPC35037
0.6019 Remote Similarity NPC90150
0.6 Remote Similarity NPC474459
0.5983 Remote Similarity NPC195841
0.5983 Remote Similarity NPC233256
0.5965 Remote Similarity NPC128698
0.5965 Remote Similarity NPC239768
0.5943 Remote Similarity NPC182106
0.5943 Remote Similarity NPC311769
0.5906 Remote Similarity NPC472458
0.5905 Remote Similarity NPC477584
0.5895 Remote Similarity NPC37792
0.5877 Remote Similarity NPC91604
0.5876 Remote Similarity NPC124384
0.5876 Remote Similarity NPC184919
0.5868 Remote Similarity NPC79238
0.5851 Remote Similarity NPC53276
0.5842 Remote Similarity NPC247325
0.5842 Remote Similarity NPC244488
0.5833 Remote Similarity NPC253645
0.5833 Remote Similarity NPC85001
0.5833 Remote Similarity NPC147835
0.5833 Remote Similarity NPC476135
0.5833 Remote Similarity NPC95920
0.5827 Remote Similarity NPC242692
0.5812 Remote Similarity NPC241879
0.581 Remote Similarity NPC471868
0.5806 Remote Similarity NPC304646
0.5806 Remote Similarity NPC28280
0.5806 Remote Similarity NPC469728
0.5806 Remote Similarity NPC219621
0.5789 Remote Similarity NPC140300
0.5789 Remote Similarity NPC469970
0.578 Remote Similarity NPC259252
0.5776 Remote Similarity NPC34193
0.5761 Remote Similarity NPC472827
0.5745 Remote Similarity NPC477740
0.5735 Remote Similarity NPC3202
0.5714 Remote Similarity NPC4166
0.5714 Remote Similarity NPC475724
0.5714 Remote Similarity NPC93027
0.5701 Remote Similarity NPC471867
0.5699 Remote Similarity NPC176621
0.5686 Remote Similarity NPC25110
0.5684 Remote Similarity NPC476682
0.5678 Remote Similarity NPC474563
0.5673 Remote Similarity NPC81306
0.5673 Remote Similarity NPC30986
0.5673 Remote Similarity NPC109546
0.5673 Remote Similarity NPC28862
0.5673 Remote Similarity NPC47982
0.5673 Remote Similarity NPC209430
0.5673 Remote Similarity NPC84694
0.5673 Remote Similarity NPC143182
0.5667 Remote Similarity NPC476756
0.5667 Remote Similarity NPC244982
0.566 Remote Similarity NPC311092
0.566 Remote Similarity NPC202389
0.5659 Remote Similarity NPC469943
0.5659 Remote Similarity NPC478138
0.5657 Remote Similarity NPC475728
0.5656 Remote Similarity NPC476290
0.5652 Remote Similarity NPC469769
0.5643 Remote Similarity NPC153007
0.5641 Remote Similarity NPC474001
0.5636 Remote Similarity NPC316186
0.5631 Remote Similarity NPC91665
0.562 Remote Similarity NPC24596
0.5619 Remote Similarity NPC234193
0.5612 Remote Similarity NPC271640
0.5607 Remote Similarity NPC470384
0.5604 Remote Similarity NPC4881
0.5604 Remote Similarity NPC104138
0.5604 Remote Similarity NPC261158
0.5604 Remote Similarity NPC24216
0.5604 Remote Similarity NPC306420
0.56 Remote Similarity NPC110615
0.56 Remote Similarity NPC470078

  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 NPC167419 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
0.7184 Intermediate Similarity NPD5771 Approved
0.7019 Intermediate Similarity NPD5769 Clinical (unspecified phase)
0.6489 Remote Similarity NPD6939 Phase 2
0.6489 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6106 Remote Similarity NPD6404 Discontinued
0.5918 Remote Similarity NPD5365 Phase 2
0.5802 Remote Similarity NPD6330 Clinical (unspecified phase)
0.5786 Remote Similarity NPD6789 Approved
0.578 Remote Similarity NPD4723 Approved
0.578 Remote Similarity NPD4722 Approved
0.5755 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6914 Discontinued
0.5702 Remote Similarity NPD2895 Discontinued
0.56 Remote Similarity NPD4243 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