Structure

Physi-Chem Properties

Molecular Weight:  464.38
Volume:  522.188
LogP:  4.977
LogD:  4.274
LogS:  -3.482
# Rotatable Bonds:  4
TPSA:  32.34
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.505
Synthetic Accessibility Score:  5.128
Fsp3:  0.774
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -5.188
MDCK Permeability:  8.23665686766617e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.901
30% Bioavailability (F30%):  0.911

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.068
Plasma Protein Binding (PPB):  75.47189331054688%
Volume Distribution (VD):  1.068
Pgp-substrate:  14.719897270202637%

ADMET: Metabolism

CYP1A2-inhibitor:  0.064
CYP1A2-substrate:  0.313
CYP2C19-inhibitor:  0.086
CYP2C19-substrate:  0.963
CYP2C9-inhibitor:  0.115
CYP2C9-substrate:  0.244
CYP2D6-inhibitor:  0.932
CYP2D6-substrate:  0.927
CYP3A4-inhibitor:  0.953
CYP3A4-substrate:  0.908

ADMET: Excretion

Clearance (CL):  8.788
Half-life (T1/2):  0.248

ADMET: Toxicity

hERG Blockers:  0.567
Human Hepatotoxicity (H-HT):  0.955
Drug-inuced Liver Injury (DILI):  0.213
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.606
Maximum Recommended Daily Dose:  0.892
Skin Sensitization:  0.547
Carcinogencity:  0.004
Eye Corrosion:  0.007
Eye Irritation:  0.012
Respiratory Toxicity:  0.974

Download Data

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

  Natural Product: NPC58200

Natural Product ID:  NPC58200
Common Name*:   Plakinamine H
IUPAC Name:   (3S,5R,9R,10R,13R,14R,17R)-3-(dimethylamino)-10,13-dimethyl-17-[(E,2R)-4-(5-methyl-1,2,3,6-tetrahydropyridin-4-yl)but-3-en-2-yl]-1,2,3,5,6,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-4-one
Synonyms:   Plakinamine H
Standard InCHIKey:  VKUXLFCVHPEFNU-JJXFVCJKSA-N
Standard InCHI:  InChI=1S/C31H48N2O/c1-20(7-8-22-15-18-32-19-21(22)2)24-11-12-25-23-9-10-27-29(34)28(33(5)6)14-17-31(27,4)26(23)13-16-30(24,25)3/h7-9,20,24-28,32H,10-19H2,1-6H3/b8-7+/t20-,24-,25+,26+,27+,28+,30-,31-/m1/s1
SMILES:  C[C@@H]([C@H]1CC[C@@H]2[C@]1(C)CC[C@H]1C2=CC[C@@H]2[C@]1(C)CC[C@@H](C2=O)N(C)C)/C=C/C1=C(C)CNCC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL488316
PubChem CID:   12049601
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 = 9.0 ug.mL-1 PMID[524877]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 61.0 ug.mL-1 PMID[524877]

☑ 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 NPC58200 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
0.8191 Intermediate Similarity NPC21667
0.81 Intermediate Similarity NPC476754
0.7822 Intermediate Similarity NPC476752
0.7822 Intermediate Similarity NPC476753
0.7788 Intermediate Similarity NPC140685
0.7685 Intermediate Similarity NPC230677
0.7653 Intermediate Similarity NPC182106
0.7653 Intermediate Similarity NPC311769
0.7545 Intermediate Similarity NPC159367
0.7526 Intermediate Similarity NPC472312
0.75 Intermediate Similarity NPC12035
0.7426 Intermediate Similarity NPC259252
0.7423 Intermediate Similarity NPC152039
0.7423 Intermediate Similarity NPC329782
0.7423 Intermediate Similarity NPC118329
0.7396 Intermediate Similarity NPC211322
0.7353 Intermediate Similarity NPC249312
0.7347 Intermediate Similarity NPC215474
0.7327 Intermediate Similarity NPC43308
0.7248 Intermediate Similarity NPC152718
0.7245 Intermediate Similarity NPC474122
0.7207 Intermediate Similarity NPC195841
0.7207 Intermediate Similarity NPC233256
0.7168 Intermediate Similarity NPC175585
0.7156 Intermediate Similarity NPC474001
0.7129 Intermediate Similarity NPC147513
0.7091 Intermediate Similarity NPC226509
0.7059 Intermediate Similarity NPC157479
0.7053 Intermediate Similarity NPC476904
0.7037 Intermediate Similarity NPC184033
0.7021 Intermediate Similarity NPC21773
0.7021 Intermediate Similarity NPC470078
0.7 Intermediate Similarity NPC34193
0.6964 Remote Similarity NPC469958
0.6931 Remote Similarity NPC171639
0.6907 Remote Similarity NPC7214
0.6875 Remote Similarity NPC98765
0.6842 Remote Similarity NPC244982
0.6842 Remote Similarity NPC476756
0.6842 Remote Similarity NPC265789
0.6842 Remote Similarity NPC110615
0.681 Remote Similarity NPC472313
0.681 Remote Similarity NPC63511
0.6809 Remote Similarity NPC182815
0.6804 Remote Similarity NPC125828
0.6796 Remote Similarity NPC24733
0.6792 Remote Similarity NPC84171
0.6783 Remote Similarity NPC24596
0.6757 Remote Similarity NPC135799
0.6757 Remote Similarity NPC239768
0.6757 Remote Similarity NPC128698
0.6752 Remote Similarity NPC79238
0.675 Remote Similarity NPC473573
0.6744 Remote Similarity NPC126458
0.6733 Remote Similarity NPC90150
0.6727 Remote Similarity NPC474164
0.6727 Remote Similarity NPC167419
0.6702 Remote Similarity NPC20610
0.6696 Remote Similarity NPC118275
0.6695 Remote Similarity NPC474452
0.6695 Remote Similarity NPC124358
0.6667 Remote Similarity NPC115023
0.6635 Remote Similarity NPC76283
0.6635 Remote Similarity NPC34811
0.6633 Remote Similarity NPC293803
0.661 Remote Similarity NPC474459
0.6609 Remote Similarity NPC185929
0.6598 Remote Similarity NPC251705
0.6566 Remote Similarity NPC174803
0.6566 Remote Similarity NPC25110
0.6566 Remote Similarity NPC259989
0.6562 Remote Similarity NPC35734
0.6562 Remote Similarity NPC282593
0.6562 Remote Similarity NPC159577
0.6525 Remote Similarity NPC72688
0.6522 Remote Similarity NPC475239
0.6505 Remote Similarity NPC283277
0.6504 Remote Similarity NPC35037
0.6495 Remote Similarity NPC234707
0.6491 Remote Similarity NPC176012
0.6491 Remote Similarity NPC476755
0.6489 Remote Similarity NPC323005
0.6476 Remote Similarity NPC152684
0.6476 Remote Similarity NPC75810
0.6471 Remote Similarity NPC143173
0.6465 Remote Similarity NPC473171
0.6442 Remote Similarity NPC477584
0.6429 Remote Similarity NPC303613
0.6429 Remote Similarity NPC474228
0.6429 Remote Similarity NPC470044
0.6429 Remote Similarity NPC470045
0.6415 Remote Similarity NPC166458
0.64 Remote Similarity NPC69408
0.6392 Remote Similarity NPC214770
0.6392 Remote Similarity NPC307176
0.6392 Remote Similarity NPC40574
0.6392 Remote Similarity NPC477856
0.6364 Remote Similarity NPC474797
0.6364 Remote Similarity NPC309852
0.6364 Remote Similarity NPC474796
0.6364 Remote Similarity NPC329866
0.6357 Remote Similarity NPC79698
0.6339 Remote Similarity NPC476903
0.6327 Remote Similarity NPC305501
0.6327 Remote Similarity NPC54123
0.6325 Remote Similarity NPC476328
0.6325 Remote Similarity NPC86906
0.6311 Remote Similarity NPC176336
0.6311 Remote Similarity NPC474509
0.6308 Remote Similarity NPC119326
0.629 Remote Similarity NPC474006
0.6289 Remote Similarity NPC139397
0.6279 Remote Similarity NPC317654
0.6279 Remote Similarity NPC96010
0.6277 Remote Similarity NPC469662
0.6275 Remote Similarity NPC470052
0.6275 Remote Similarity NPC82635
0.626 Remote Similarity NPC246904
0.625 Remote Similarity NPC311164
0.625 Remote Similarity NPC272732
0.6239 Remote Similarity NPC119329
0.6231 Remote Similarity NPC478136
0.6224 Remote Similarity NPC2634
0.6224 Remote Similarity NPC265782
0.6224 Remote Similarity NPC251929
0.6224 Remote Similarity NPC260040
0.6218 Remote Similarity NPC476918
0.6218 Remote Similarity NPC476276
0.6216 Remote Similarity NPC247316
0.6216 Remote Similarity NPC93027
0.6214 Remote Similarity NPC170793
0.6211 Remote Similarity NPC469970
0.62 Remote Similarity NPC255021
0.6195 Remote Similarity NPC247220
0.619 Remote Similarity NPC477583
0.6186 Remote Similarity NPC142754
0.6186 Remote Similarity NPC296697
0.6186 Remote Similarity NPC82477
0.6186 Remote Similarity NPC39157
0.6176 Remote Similarity NPC91665
0.617 Remote Similarity NPC197238
0.617 Remote Similarity NPC202118
0.6162 Remote Similarity NPC181204
0.6146 Remote Similarity NPC43300
0.6139 Remote Similarity NPC255650
0.6122 Remote Similarity NPC286814
0.6121 Remote Similarity NPC474582
0.6106 Remote Similarity NPC174117
0.6105 Remote Similarity NPC53276
0.6095 Remote Similarity NPC477582
0.6095 Remote Similarity NPC4166
0.6095 Remote Similarity NPC257962
0.6087 Remote Similarity NPC91604
0.6082 Remote Similarity NPC176107
0.6082 Remote Similarity NPC220210
0.6082 Remote Similarity NPC20181
0.6078 Remote Similarity NPC469793
0.6078 Remote Similarity NPC469796
0.6075 Remote Similarity NPC57163
0.6075 Remote Similarity NPC116881
0.6074 Remote Similarity NPC473962
0.6061 Remote Similarity NPC473442
0.6061 Remote Similarity NPC120167
0.605 Remote Similarity NPC476926
0.605 Remote Similarity NPC474695
0.6038 Remote Similarity NPC311092
0.6038 Remote Similarity NPC477581
0.6036 Remote Similarity NPC473056
0.6033 Remote Similarity NPC95920
0.6033 Remote Similarity NPC147835
0.6033 Remote Similarity NPC253645
0.6033 Remote Similarity NPC85001
0.602 Remote Similarity NPC271640
0.602 Remote Similarity NPC310992
0.6019 Remote Similarity NPC470557
0.6017 Remote Similarity NPC241879
0.6 Remote Similarity NPC225467
0.6 Remote Similarity NPC472544
0.6 Remote Similarity NPC190035
0.6 Remote Similarity NPC250632
0.5981 Remote Similarity NPC83569
0.5981 Remote Similarity NPC69279
0.5979 Remote Similarity NPC92327
0.5979 Remote Similarity NPC96812
0.5979 Remote Similarity NPC189917
0.5979 Remote Similarity NPC39462
0.5979 Remote Similarity NPC107704
0.5979 Remote Similarity NPC168824
0.5966 Remote Similarity NPC476921
0.5963 Remote Similarity NPC476141
0.596 Remote Similarity NPC138409
0.5952 Remote Similarity NPC477121
0.5943 Remote Similarity NPC147066
0.5941 Remote Similarity NPC474488
0.5932 Remote Similarity NPC50815
0.5932 Remote Similarity NPC471083
0.5926 Remote Similarity NPC87552
0.5909 Remote Similarity NPC93778
0.5909 Remote Similarity NPC75315
0.5909 Remote Similarity NPC163016

  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 NPC58200 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
0.7075 Intermediate Similarity NPD5769 Clinical (unspecified phase)
0.6931 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6531 Remote Similarity NPD4687 Approved
0.6531 Remote Similarity NPD4058 Approved
0.6531 Remote Similarity NPD5733 Approved
0.6392 Remote Similarity NPD4747 Approved
0.6354 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6339 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6327 Remote Similarity NPD5365 Phase 2
0.6327 Remote Similarity NPD5276 Approved
0.6289 Remote Similarity NPD4137 Phase 3
0.6224 Remote Similarity NPD4691 Approved
0.6214 Remote Similarity NPD7155 Clinical (unspecified phase)
0.6186 Remote Similarity NPD7333 Discontinued
0.5985 Remote Similarity NPD6330 Clinical (unspecified phase)
0.5932 Remote Similarity NPD6024 Approved
0.5932 Remote Similarity NPD6027 Approved
0.5877 Remote Similarity NPD5771 Approved
0.5862 Remote Similarity NPD4655 Approved
0.5862 Remote Similarity NPD4657 Approved
0.581 Remote Similarity NPD1402 Approved
0.5802 Remote Similarity NPD3836 Clinical (unspecified phase)
0.5794 Remote Similarity NPD8028 Phase 2
0.578 Remote Similarity NPD4786 Approved
0.576 Remote Similarity NPD7336 Phase 2
0.576 Remote Similarity NPD7335 Phase 2
0.576 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5752 Remote Similarity NPD6934 Discontinued
0.5752 Remote Similarity NPD4096 Approved
0.5741 Remote Similarity NPD4223 Phase 3
0.5741 Remote Similarity NPD4221 Approved
0.5727 Remote Similarity NPD5329 Approved
0.5702 Remote Similarity NPD7812 Clinical (unspecified phase)
0.569 Remote Similarity NPD4094 Approved
0.5676 Remote Similarity NPD5280 Approved
0.5676 Remote Similarity NPD4694 Approved
0.5676 Remote Similarity NPD6098 Approved
0.566 Remote Similarity NPD4777 Suspended
0.566 Remote Similarity NPD4776 Phase 2
0.5649 Remote Similarity NPD6908 Approved
0.5649 Remote Similarity NPD6909 Approved
0.5649 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5636 Remote Similarity NPD4197 Approved
0.563 Remote Similarity NPD6404 Discontinued
0.5614 Remote Similarity NPD5207 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