Structure

Physi-Chem Properties

Molecular Weight:  438.4
Volume:  501.374
LogP:  6.251
LogD:  6.198
LogS:  -6.477
# Rotatable Bonds:  4
TPSA:  29.26
# H-Bond Aceptor:  2
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.497
Synthetic Accessibility Score:  5.194
Fsp3:  0.867
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:  -4.797
MDCK Permeability:  9.857954864855856e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.163
30% Bioavailability (F30%):  0.403

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.054
Plasma Protein Binding (PPB):  96.1632308959961%
Volume Distribution (VD):  0.497
Pgp-substrate:  2.0790579319000244%

ADMET: Metabolism

CYP1A2-inhibitor:  0.045
CYP1A2-substrate:  0.122
CYP2C19-inhibitor:  0.045
CYP2C19-substrate:  0.967
CYP2C9-inhibitor:  0.102
CYP2C9-substrate:  0.064
CYP2D6-inhibitor:  0.917
CYP2D6-substrate:  0.915
CYP3A4-inhibitor:  0.723
CYP3A4-substrate:  0.803

ADMET: Excretion

Clearance (CL):  6.021
Half-life (T1/2):  0.1

ADMET: Toxicity

hERG Blockers:  0.276
Human Hepatotoxicity (H-HT):  0.17
Drug-inuced Liver Injury (DILI):  0.035
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.24
Maximum Recommended Daily Dose:  0.265
Skin Sensitization:  0.044
Carcinogencity:  0.005
Eye Corrosion:  0.004
Eye Irritation:  0.016
Respiratory Toxicity:  0.853

Download Data

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

  Natural Product: NPC474122

Natural Product ID:  NPC474122
Common Name*:   Plakinamine J
IUPAC Name:   (4R,5R,9R,10R,13R,14R,17R)-10,13-dimethyl-17-[(2R)-1-(1-methyl-3-propan-2-ylpyrrolidin-2-yl)propan-2-yl]-4,5,6,9,11,12,14,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-4-amine
Synonyms:   Plakinamine J
Standard InCHIKey:  OWWFXCRBYSQOCJ-JWIPIMPKSA-N
Standard InCHI:  InChI=1S/C30H50N2/c1-19(2)21-14-17-32(6)28(21)18-20(3)23-11-12-24-22-9-10-26-27(31)8-7-15-29(26,4)25(22)13-16-30(23,24)5/h7-9,19-21,23-28H,10-18,31H2,1-6H3/t20-,21?,23-,24+,25+,26+,27-,28?,29-,30-/m1/s1
SMILES:  CC(C1CCN(C1C[C@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1C2=CC[C@@H]2[C@]1(C)CC=C[C@H]2N)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL462453
PubChem CID:   11293552
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
NPO17725 Corticium niger Species Plakinidae Eukaryota n.a. Philippine n.a. PMID[14695791]
NPO17725 Corticium niger Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[25338277]
NPO17725 Corticium niger Species Plakinidae 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
NPT393 Cell Line HCT-116 Homo sapiens IC50 = 6100.0 nM PMID[448922]

☑ 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 NPC474122 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
0.9231 High Similarity NPC152039
0.9231 High Similarity NPC118329
0.9114 High Similarity NPC472312
0.8987 High Similarity NPC329782
0.8831 High Similarity NPC7214
0.8395 Intermediate Similarity NPC12035
0.8313 Intermediate Similarity NPC171639
0.8312 Intermediate Similarity NPC265789
0.8312 Intermediate Similarity NPC21773
0.8272 Intermediate Similarity NPC211322
0.8101 Intermediate Similarity NPC476904
0.7907 Intermediate Similarity NPC24733
0.7778 Intermediate Similarity NPC125828
0.7765 Intermediate Similarity NPC283277
0.7558 Intermediate Similarity NPC215474
0.747 Intermediate Similarity NPC259989
0.747 Intermediate Similarity NPC174803
0.7273 Intermediate Similarity NPC472544
0.7245 Intermediate Similarity NPC58200
0.7143 Intermediate Similarity NPC43308
0.7111 Intermediate Similarity NPC147513
0.7097 Intermediate Similarity NPC84171
0.7079 Intermediate Similarity NPC21667
0.7041 Intermediate Similarity NPC135799
0.7033 Intermediate Similarity NPC166458
0.7033 Intermediate Similarity NPC157479
0.6962 Remote Similarity NPC53276
0.6923 Remote Similarity NPC75810
0.6923 Remote Similarity NPC472313
0.6893 Remote Similarity NPC159367
0.6875 Remote Similarity NPC469970
0.6857 Remote Similarity NPC79238
0.6837 Remote Similarity NPC167419
0.6837 Remote Similarity NPC474164
0.6792 Remote Similarity NPC474452
0.6768 Remote Similarity NPC91604
0.6753 Remote Similarity NPC469769
0.6739 Remote Similarity NPC152684
0.6709 Remote Similarity NPC219621
0.6701 Remote Similarity NPC476754
0.6698 Remote Similarity NPC474459
0.6667 Remote Similarity NPC90150
0.6634 Remote Similarity NPC118275
0.663 Remote Similarity NPC471867
0.6627 Remote Similarity NPC271640
0.6579 Remote Similarity NPC123194
0.6569 Remote Similarity NPC176012
0.6538 Remote Similarity NPC195841
0.6538 Remote Similarity NPC86906
0.6538 Remote Similarity NPC233256
0.6538 Remote Similarity NPC472830
0.6456 Remote Similarity NPC21781
0.6449 Remote Similarity NPC63511
0.6436 Remote Similarity NPC140685
0.6429 Remote Similarity NPC93027
0.6429 Remote Similarity NPC476753
0.6429 Remote Similarity NPC476752
0.64 Remote Similarity NPC476903
0.6386 Remote Similarity NPC37792
0.6383 Remote Similarity NPC182106
0.6383 Remote Similarity NPC311769
0.6381 Remote Similarity NPC230677
0.6355 Remote Similarity NPC147835
0.6355 Remote Similarity NPC175585
0.6355 Remote Similarity NPC95920
0.6355 Remote Similarity NPC85001
0.6355 Remote Similarity NPC253645
0.6341 Remote Similarity NPC476559
0.6329 Remote Similarity NPC231129
0.6321 Remote Similarity NPC46981
0.6311 Remote Similarity NPC474582
0.6306 Remote Similarity NPC304646
0.6306 Remote Similarity NPC28280
0.6304 Remote Similarity NPC257962
0.63 Remote Similarity NPC311164
0.63 Remote Similarity NPC272732
0.6292 Remote Similarity NPC25110
0.6279 Remote Similarity NPC472543
0.6277 Remote Similarity NPC57163
0.6277 Remote Similarity NPC116881
0.625 Remote Similarity NPC82919
0.625 Remote Similarity NPC50815
0.6226 Remote Similarity NPC474695
0.622 Remote Similarity NPC474086
0.6214 Remote Similarity NPC128698
0.6214 Remote Similarity NPC239768
0.6186 Remote Similarity NPC259252
0.6176 Remote Similarity NPC140300
0.6173 Remote Similarity NPC311809
0.6154 Remote Similarity NPC470893
0.6146 Remote Similarity NPC56107
0.6132 Remote Similarity NPC212874
0.6095 Remote Similarity NPC471083
0.6095 Remote Similarity NPC152718
0.6095 Remote Similarity NPC247060
0.6087 Remote Similarity NPC57599
0.6058 Remote Similarity NPC275686
0.6049 Remote Similarity NPC472827
0.6038 Remote Similarity NPC241879
0.6019 Remote Similarity NPC25340
0.6019 Remote Similarity NPC184033
0.6 Remote Similarity NPC34193
0.6 Remote Similarity NPC17518
0.6 Remote Similarity NPC475696
0.6 Remote Similarity NPC474001
0.6 Remote Similarity NPC474415
0.6 Remote Similarity NPC474528
0.5981 Remote Similarity NPC469958
0.598 Remote Similarity NPC25033
0.598 Remote Similarity NPC119225
0.598 Remote Similarity NPC476261
0.598 Remote Similarity NPC471635
0.598 Remote Similarity NPC470382
0.5977 Remote Similarity NPC184919
0.5977 Remote Similarity NPC138409
0.5976 Remote Similarity NPC317778
0.596 Remote Similarity NPC249312
0.5952 Remote Similarity NPC473959
0.5943 Remote Similarity NPC226509
0.5934 Remote Similarity NPC476308
0.593 Remote Similarity NPC176107
0.5922 Remote Similarity NPC289140
0.5921 Remote Similarity NPC200129
0.5909 Remote Similarity NPC120167
0.5909 Remote Similarity NPC473442
0.5895 Remote Similarity NPC471868
0.5888 Remote Similarity NPC90538
0.5888 Remote Similarity NPC98765
0.5876 Remote Similarity NPC76283
0.5867 Remote Similarity NPC124851
0.5862 Remote Similarity NPC35037
0.5854 Remote Similarity NPC474455
0.5854 Remote Similarity NPC474420
0.5854 Remote Similarity NPC475716
0.5854 Remote Similarity NPC474454
0.5833 Remote Similarity NPC145715
0.5814 Remote Similarity NPC176171
0.5814 Remote Similarity NPC92327
0.5802 Remote Similarity NPC470370
0.5802 Remote Similarity NPC470369
0.5802 Remote Similarity NPC474457
0.5802 Remote Similarity NPC173815
0.5795 Remote Similarity NPC124384
0.5795 Remote Similarity NPC245223
0.5795 Remote Similarity NPC182815
0.5789 Remote Similarity NPC22765
0.5785 Remote Similarity NPC317654
0.5785 Remote Similarity NPC96010
0.578 Remote Similarity NPC55462
0.5778 Remote Similarity NPC470044
0.5778 Remote Similarity NPC470045
0.5752 Remote Similarity NPC56796
0.575 Remote Similarity NPC469770
0.5741 Remote Similarity NPC474583
0.5739 Remote Similarity NPC246904
0.5738 Remote Similarity NPC478136
0.5733 Remote Similarity NPC323445
0.5732 Remote Similarity NPC324944
0.573 Remote Similarity NPC475728
0.5728 Remote Similarity NPC280710
0.5728 Remote Similarity NPC243985
0.5714 Remote Similarity NPC478138
0.5696 Remote Similarity NPC127944
0.5696 Remote Similarity NPC472828
0.5688 Remote Similarity NPC119329
0.5682 Remote Similarity NPC20610
0.5667 Remote Similarity NPC470078
0.5667 Remote Similarity NPC115023
0.5667 Remote Similarity NPC476329
0.5652 Remote Similarity NPC471468
0.5644 Remote Similarity NPC323156
0.5636 Remote Similarity NPC476328
0.5632 Remote Similarity NPC474456
0.5625 Remote Similarity NPC231986
0.5618 Remote Similarity NPC472831
0.5604 Remote Similarity NPC251705
0.56 Remote Similarity NPC49088
0.56 Remote Similarity NPC86683

  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 NPC474122 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
0.7195 Intermediate Similarity NPD5365 Phase 2
0.6279 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6279 Remote Similarity NPD6939 Phase 2
0.5922 Remote Similarity NPD1738 Approved
0.5921 Remote Similarity NPD4834 Discontinued
0.5893 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5893 Remote Similarity NPD7336 Phase 2
0.5893 Remote Similarity NPD7335 Phase 2
0.5842 Remote Similarity NPD4543 Discontinued
0.5833 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5769 Remote Similarity NPD5964 Phase 2
0.5769 Remote Similarity NPD5963 Phase 2
0.5769 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5728 Remote Similarity NPD3982 Approved
0.5728 Remote Similarity NPD5771 Approved
0.5728 Remote Similarity NPD3980 Approved
0.5658 Remote Similarity NPD5379 Clinical (unspecified phase)
0.5657 Remote Similarity NPD3099 Discontinued
0.5644 Remote Similarity NPD771 Phase 3
0.5641 Remote Similarity NPD5793 Discontinued
0.5625 Remote Similarity NPD3727 Discontinued
0.5612 Remote Similarity NPD5178 Approved
0.5607 Remote Similarity NPD1946 Clinical (unspecified phase)
0.56 Remote Similarity NPD4145 Approved
0.56 Remote Similarity NPD4146 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