Structure

Physi-Chem Properties

Molecular Weight:  498.42
Volume:  553.547
LogP:  5.124
LogD:  5.582
LogS:  -5.487
# Rotatable Bonds:  7
TPSA:  50.36
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.331
Synthetic Accessibility Score:  5.177
Fsp3:  0.906
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:  -5.092
MDCK Permeability:  3.204953463864513e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.01
Human Intestinal Absorption (HIA):  0.031
20% Bioavailability (F20%):  0.147
30% Bioavailability (F30%):  0.95

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.007
Plasma Protein Binding (PPB):  85.65887451171875%
Volume Distribution (VD):  0.506
Pgp-substrate:  2.059680700302124%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.057
CYP2C19-substrate:  0.93
CYP2C9-inhibitor:  0.075
CYP2C9-substrate:  0.048
CYP2D6-inhibitor:  0.903
CYP2D6-substrate:  0.893
CYP3A4-inhibitor:  0.789
CYP3A4-substrate:  0.743

ADMET: Excretion

Clearance (CL):  3.362
Half-life (T1/2):  0.078

ADMET: Toxicity

hERG Blockers:  0.767
Human Hepatotoxicity (H-HT):  0.979
Drug-inuced Liver Injury (DILI):  0.045
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.627
Maximum Recommended Daily Dose:  0.463
Skin Sensitization:  0.125
Carcinogencity:  0.001
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.948

Download Data

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

  Natural Product: NPC474459

Natural Product ID:  NPC474459
Common Name*:   24,25-Dihydroplakinamine K
IUPAC Name:   [(3R,4R,5R,9R,10R,13R,14R,17R)-10,13-dimethyl-3-(methylamino)-17-[(2R)-1-(3-propan-2-ylpyrrolidin-2-yl)propan-2-yl]-2,3,4,5,6,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-4-yl] acetate
Synonyms:   24,25-Dihydroplakinamine K
Standard InCHIKey:  RWTFLBCUUBVVCW-XGHKHTGLSA-N
Standard InCHI:  InChI=1S/C32H54N2O2/c1-19(2)22-14-17-34-29(22)18-20(3)24-10-11-25-23-8-9-27-30(36-21(4)35)28(33-7)13-16-32(27,6)26(23)12-15-31(24,25)5/h8,19-20,22,24-30,33-34H,9-18H2,1-7H3/t20-,22?,24-,25+,26+,27+,28-,29?,30-,31-,32-/m1/s1
SMILES:  CN[C@@H]1CC[C@]2([C@H]([C@H]1OC(=O)C)CC=C1[C@@H]2CC[C@]2([C@H]1CC[C@@H]2[C@@H](CC1NCCC1C(C)C)C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL469288
PubChem CID:   11260519
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 = 1400.0 nM PMID[486852]

☑ 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 NPC474459 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
0.9903 High Similarity NPC474452
0.9709 High Similarity NPC472313
0.8889 High Similarity NPC79238
0.8426 Intermediate Similarity NPC195841
0.8426 Intermediate Similarity NPC86906
0.8426 Intermediate Similarity NPC233256
0.7965 Intermediate Similarity NPC72753
0.7963 Intermediate Similarity NPC239768
0.7963 Intermediate Similarity NPC128698
0.7895 Intermediate Similarity NPC66862
0.7685 Intermediate Similarity NPC476903
0.7672 Intermediate Similarity NPC469968
0.7672 Intermediate Similarity NPC80834
0.7642 Intermediate Similarity NPC237286
0.7632 Intermediate Similarity NPC159367
0.7583 Intermediate Similarity NPC35037
0.7547 Intermediate Similarity NPC84171
0.7479 Intermediate Similarity NPC304646
0.7479 Intermediate Similarity NPC28280
0.7456 Intermediate Similarity NPC36497
0.7381 Intermediate Similarity NPC478136
0.7368 Intermediate Similarity NPC119329
0.7353 Intermediate Similarity NPC329782
0.7297 Intermediate Similarity NPC474164
0.7282 Intermediate Similarity NPC472312
0.7265 Intermediate Similarity NPC85001
0.7265 Intermediate Similarity NPC147835
0.7265 Intermediate Similarity NPC253645
0.7265 Intermediate Similarity NPC95920
0.7258 Intermediate Similarity NPC478138
0.7258 Intermediate Similarity NPC472458
0.7241 Intermediate Similarity NPC25340
0.7238 Intermediate Similarity NPC75810
0.7203 Intermediate Similarity NPC63511
0.7193 Intermediate Similarity NPC176012
0.7184 Intermediate Similarity NPC118329
0.7184 Intermediate Similarity NPC152039
0.7177 Intermediate Similarity NPC242692
0.7165 Intermediate Similarity NPC96010
0.7165 Intermediate Similarity NPC317654
0.713 Intermediate Similarity NPC474583
0.713 Intermediate Similarity NPC323156
0.713 Intermediate Similarity NPC241879
0.7083 Intermediate Similarity NPC124358
0.7083 Intermediate Similarity NPC56796
0.7043 Intermediate Similarity NPC471083
0.7025 Intermediate Similarity NPC478137
0.7018 Intermediate Similarity NPC135799
0.6957 Remote Similarity NPC118275
0.6949 Remote Similarity NPC46981
0.6942 Remote Similarity NPC477291
0.6937 Remote Similarity NPC93027
0.693 Remote Similarity NPC91604
0.6911 Remote Similarity NPC165396
0.6903 Remote Similarity NPC289140
0.6887 Remote Similarity NPC139206
0.687 Remote Similarity NPC478139
0.6864 Remote Similarity NPC55462
0.6838 Remote Similarity NPC98765
0.6827 Remote Similarity NPC44083
0.6827 Remote Similarity NPC153987
0.678 Remote Similarity NPC477001
0.678 Remote Similarity NPC212874
0.678 Remote Similarity NPC477000
0.6774 Remote Similarity NPC470538
0.6762 Remote Similarity NPC12035
0.6741 Remote Similarity NPC297058
0.6699 Remote Similarity NPC7214
0.6698 Remote Similarity NPC474122
0.6697 Remote Similarity NPC474970
0.6696 Remote Similarity NPC140300
0.6667 Remote Similarity NPC476756
0.6667 Remote Similarity NPC244982
0.6642 Remote Similarity NPC287885
0.664 Remote Similarity NPC476955
0.6639 Remote Similarity NPC472359
0.6639 Remote Similarity NPC475239
0.6637 Remote Similarity NPC470224
0.6636 Remote Similarity NPC478104
0.6636 Remote Similarity NPC215474
0.6615 Remote Similarity NPC296686
0.661 Remote Similarity NPC50815
0.661 Remote Similarity NPC58200
0.6607 Remote Similarity NPC471896
0.6606 Remote Similarity NPC470223
0.6594 Remote Similarity NPC478140
0.6577 Remote Similarity NPC28227
0.6574 Remote Similarity NPC21667
0.6545 Remote Similarity NPC264127
0.6545 Remote Similarity NPC286153
0.6542 Remote Similarity NPC290495
0.6542 Remote Similarity NPC195334
0.6525 Remote Similarity NPC39473
0.6522 Remote Similarity NPC311164
0.6522 Remote Similarity NPC119225
0.6522 Remote Similarity NPC470382
0.6522 Remote Similarity NPC476261
0.6522 Remote Similarity NPC272732
0.6522 Remote Similarity NPC25033
0.6522 Remote Similarity NPC471635
0.6514 Remote Similarity NPC100391
0.6509 Remote Similarity NPC211322
0.6509 Remote Similarity NPC47808
0.6509 Remote Similarity NPC305835
0.6505 Remote Similarity NPC476904
0.65 Remote Similarity NPC470596
0.6491 Remote Similarity NPC38232
0.6491 Remote Similarity NPC473678
0.6486 Remote Similarity NPC43308
0.6481 Remote Similarity NPC286786
0.6471 Remote Similarity NPC247060
0.646 Remote Similarity NPC148414
0.646 Remote Similarity NPC111585
0.646 Remote Similarity NPC175628
0.6455 Remote Similarity NPC24733
0.6449 Remote Similarity NPC304194
0.6446 Remote Similarity NPC258130
0.6444 Remote Similarity NPC15249
0.6444 Remote Similarity NPC25455
0.6441 Remote Similarity NPC275686
0.6435 Remote Similarity NPC476754
0.6429 Remote Similarity NPC97884
0.6429 Remote Similarity NPC470613
0.6429 Remote Similarity NPC472220
0.6429 Remote Similarity NPC470612
0.6422 Remote Similarity NPC132386
0.6422 Remote Similarity NPC171639
0.641 Remote Similarity NPC473537
0.6404 Remote Similarity NPC177641
0.6404 Remote Similarity NPC26888
0.6397 Remote Similarity NPC122819
0.6393 Remote Similarity NPC169375
0.6389 Remote Similarity NPC108476
0.6385 Remote Similarity NPC470277
0.6372 Remote Similarity NPC474889
0.6372 Remote Similarity NPC473647
0.6356 Remote Similarity NPC252564
0.6356 Remote Similarity NPC475249
0.635 Remote Similarity NPC147753
0.635 Remote Similarity NPC150057
0.6348 Remote Similarity NPC476753
0.6348 Remote Similarity NPC476752
0.6341 Remote Similarity NPC470595
0.6339 Remote Similarity NPC142361
0.6339 Remote Similarity NPC167877
0.6339 Remote Similarity NPC474684
0.6325 Remote Similarity NPC54248
0.6325 Remote Similarity NPC304899
0.6325 Remote Similarity NPC276103
0.6325 Remote Similarity NPC253115
0.6325 Remote Similarity NPC475178
0.6316 Remote Similarity NPC48886
0.6316 Remote Similarity NPC473269
0.6316 Remote Similarity NPC265275
0.6316 Remote Similarity NPC94881
0.6311 Remote Similarity NPC230677
0.6311 Remote Similarity NPC477292
0.6311 Remote Similarity NPC21773
0.6306 Remote Similarity NPC147513
0.6306 Remote Similarity NPC191965
0.6303 Remote Similarity NPC201712
0.6296 Remote Similarity NPC206735
0.6296 Remote Similarity NPC269791
0.6293 Remote Similarity NPC474922
0.6293 Remote Similarity NPC159410
0.629 Remote Similarity NPC218602
0.6283 Remote Similarity NPC473879
0.6283 Remote Similarity NPC474845
0.6281 Remote Similarity NPC90538
0.6279 Remote Similarity NPC470276
0.6273 Remote Similarity NPC473742
0.6273 Remote Similarity NPC5280
0.6271 Remote Similarity NPC292819
0.6271 Remote Similarity NPC240650
0.626 Remote Similarity NPC476504
0.625 Remote Similarity NPC470050
0.625 Remote Similarity NPC470051
0.625 Remote Similarity NPC84121
0.625 Remote Similarity NPC91525
0.625 Remote Similarity NPC10005
0.625 Remote Similarity NPC157479
0.625 Remote Similarity NPC137306
0.625 Remote Similarity NPC195640
0.625 Remote Similarity NPC9892
0.625 Remote Similarity NPC474348
0.625 Remote Similarity NPC329943
0.625 Remote Similarity NPC475518
0.625 Remote Similarity NPC325594
0.625 Remote Similarity NPC201359
0.6239 Remote Similarity NPC142163
0.6239 Remote Similarity NPC155985
0.6239 Remote Similarity NPC279974
0.6231 Remote Similarity NPC475340
0.623 Remote Similarity NPC31430
0.623 Remote Similarity NPC85593
0.623 Remote Similarity NPC44514
0.6228 Remote Similarity NPC177141
0.6228 Remote Similarity NPC474570
0.6228 Remote Similarity NPC472240
0.6228 Remote Similarity NPC474704

  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 NPC474459 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
0.7521 Intermediate Similarity NPD7336 Phase 2
0.7521 Intermediate Similarity NPD7335 Phase 2
0.7521 Intermediate Similarity NPD7337 Clinical (unspecified phase)
0.719 Intermediate Similarity NPD7754 Approved
0.719 Intermediate Similarity NPD7755 Approved
0.6942 Remote Similarity NPD8077 Approved
0.6942 Remote Similarity NPD8078 Approved
0.6903 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6697 Remote Similarity NPD8308 Discontinued
0.6695 Remote Similarity NPD7987 Approved
0.6695 Remote Similarity NPD7986 Approved
0.6695 Remote Similarity NPD7911 Approved
0.6695 Remote Similarity NPD7912 Approved
0.6583 Remote Similarity NPD8040 Discontinued
0.6529 Remote Similarity NPD7989 Approved
0.6529 Remote Similarity NPD7990 Approved
0.6512 Remote Similarity NPD6909 Approved
0.6512 Remote Similarity NPD6908 Approved
0.641 Remote Similarity NPD7919 Phase 3
0.641 Remote Similarity NPD7920 Phase 3
0.6397 Remote Similarity NPD8449 Approved
0.6393 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6356 Remote Similarity NPD8088 Phase 1
0.635 Remote Similarity NPD8450 Suspended
0.6321 Remote Similarity NPD8143 Approved
0.6321 Remote Similarity NPD8144 Approved
0.6283 Remote Similarity NPD6903 Approved
0.625 Remote Similarity NPD6409 Approved
0.625 Remote Similarity NPD5330 Approved
0.625 Remote Similarity NPD7521 Approved
0.625 Remote Similarity NPD6684 Approved
0.625 Remote Similarity NPD7334 Approved
0.625 Remote Similarity NPD7146 Approved
0.6239 Remote Similarity NPD6356 Clinical (unspecified phase)
0.6228 Remote Similarity NPD6051 Approved
0.614 Remote Similarity NPD6672 Approved
0.614 Remote Similarity NPD5737 Approved
0.614 Remote Similarity NPD7513 Clinical (unspecified phase)
0.6103 Remote Similarity NPD8337 Approved
0.6103 Remote Similarity NPD8336 Approved
0.6068 Remote Similarity NPD6399 Phase 3
0.6048 Remote Similarity NPD6920 Discontinued
0.6045 Remote Similarity NPD7122 Discontinued
0.6017 Remote Similarity NPD6001 Approved
0.6017 Remote Similarity NPD5707 Approved
0.5969 Remote Similarity NPD8298 Phase 2
0.5965 Remote Similarity NPD6098 Approved
0.5952 Remote Similarity NPD6415 Discontinued
0.5932 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5929 Remote Similarity NPD8338 Approved
0.592 Remote Similarity NPD6008 Approved
0.5882 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5882 Remote Similarity NPD7748 Approved
0.5882 Remote Similarity NPD5771 Approved
0.5882 Remote Similarity NPD7900 Approved
0.5865 Remote Similarity NPD7517 Approved
0.5865 Remote Similarity NPD7518 Approved
0.5865 Remote Similarity NPD7519 Approved
0.5856 Remote Similarity NPD7525 Registered
0.5847 Remote Similarity NPD8035 Phase 2
0.5847 Remote Similarity NPD8034 Phase 2
0.5833 Remote Similarity NPD7339 Approved
0.5833 Remote Similarity NPD6942 Approved
0.5827 Remote Similarity NPD7320 Approved
0.582 Remote Similarity NPD7638 Approved
0.5812 Remote Similarity NPD6080 Approved
0.5812 Remote Similarity NPD6673 Approved
0.5812 Remote Similarity NPD6904 Approved
0.5812 Remote Similarity NPD5328 Approved
0.5794 Remote Similarity NPD6675 Approved
0.5794 Remote Similarity NPD7128 Approved
0.5794 Remote Similarity NPD5739 Approved
0.5794 Remote Similarity NPD6402 Approved
0.5789 Remote Similarity NPD4786 Approved
0.5786 Remote Similarity NPD6914 Discontinued
0.5786 Remote Similarity NPD7751 Phase 1
0.5772 Remote Similarity NPD7639 Approved
0.5772 Remote Similarity NPD8418 Phase 2
0.5772 Remote Similarity NPD7640 Approved
0.5763 Remote Similarity NPD5207 Approved
0.5739 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5738 Remote Similarity NPD7902 Approved
0.5738 Remote Similarity NPD6084 Phase 2
0.5738 Remote Similarity NPD6083 Phase 2
0.5726 Remote Similarity NPD5208 Approved
0.5714 Remote Similarity NPD6079 Approved
0.5703 Remote Similarity NPD6881 Approved
0.5703 Remote Similarity NPD6899 Approved
0.5702 Remote Similarity NPD7991 Discontinued
0.5701 Remote Similarity NPD5365 Phase 2
0.5692 Remote Similarity NPD8130 Phase 1
0.569 Remote Similarity NPD3618 Phase 1
0.5669 Remote Similarity NPD7333 Discontinued
0.5659 Remote Similarity NPD6373 Approved
0.5659 Remote Similarity NPD6372 Approved
0.5655 Remote Similarity NPD6623 Phase 3
0.5649 Remote Similarity NPD8297 Approved
0.5636 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5697 Approved
0.5625 Remote Similarity NPD5701 Approved
0.5625 Remote Similarity NPD7645 Phase 2
0.5616 Remote Similarity NPD6333 Approved
0.5616 Remote Similarity NPD6334 Approved
0.5615 Remote Similarity NPD7102 Approved
0.5615 Remote Similarity NPD7290 Approved
0.5615 Remote Similarity NPD6883 Approved
0.5614 Remote Similarity NPD3667 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