Structure

Physi-Chem Properties

Molecular Weight:  466.39
Volume:  524.824
LogP:  5.975
LogD:  5.863
LogS:  -6.187
# Rotatable Bonds:  4
TPSA:  35.83
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  5
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.469
Synthetic Accessibility Score:  5.173
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:  -4.776
MDCK Permeability:  1.0642468623700552e-05
Pgp-inhibitor:  0.952
Pgp-substrate:  0.2
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.874
30% Bioavailability (F30%):  0.541

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.01
Plasma Protein Binding (PPB):  91.34053802490234%
Volume Distribution (VD):  1.209
Pgp-substrate:  2.0813634395599365%

ADMET: Metabolism

CYP1A2-inhibitor:  0.063
CYP1A2-substrate:  0.281
CYP2C19-inhibitor:  0.038
CYP2C19-substrate:  0.975
CYP2C9-inhibitor:  0.094
CYP2C9-substrate:  0.2
CYP2D6-inhibitor:  0.955
CYP2D6-substrate:  0.917
CYP3A4-inhibitor:  0.621
CYP3A4-substrate:  0.887

ADMET: Excretion

Clearance (CL):  6.565
Half-life (T1/2):  0.082

ADMET: Toxicity

hERG Blockers:  0.554
Human Hepatotoxicity (H-HT):  0.347
Drug-inuced Liver Injury (DILI):  0.097
AMES Toxicity:  0.001
Rat Oral Acute Toxicity:  0.37
Maximum Recommended Daily Dose:  0.316
Skin Sensitization:  0.448
Carcinogencity:  0.005
Eye Corrosion:  0.004
Eye Irritation:  0.024
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC25340

Natural Product ID:  NPC25340
Common Name*:   Lokysterolamine A
IUPAC Name:   (3S,4R,5R,9R,10R,13R,14R,17R)-3-(dimethylamino)-10,13-dimethyl-17-[(2R)-1-(4-propan-2-ylidene-2,3-dihydropyrrol-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:  
Standard InCHIKey:  VIMZHTFJEDRKBC-GQYVRWDISA-N
Standard InCHI:  InChI=1S/C31H50N2O/c1-19(2)21-14-17-32-27(21)18-20(3)23-10-11-24-22-8-9-26-29(34)28(33(6)7)13-16-31(26,5)25(22)12-15-30(23,24)4/h8,20,23-26,28-29,34H,9-18H2,1-7H3/t20-,23-,24+,25+,26+,28+,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)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL474920
PubChem CID:   157832
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]
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
NPT111 Cell Line K562 Homo sapiens LC50 = 0.9 ug.mL-1 PMID[456643]
NPT168 Cell Line P388 Mus musculus IC50 = 0.5 ug.mL-1 PMID[456644]
NPT81 Cell Line A549 Homo sapiens IC50 = 0.5 ug.mL-1 PMID[456644]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 1.0 ug.mL-1 PMID[456644]
NPT170 Cell Line SK-MEL-28 Homo sapiens IC50 = 5.0 ug.mL-1 PMID[456644]
NPT20 Organism Candida albicans Candida albicans IZ = 9.0 mm PMID[456643]
NPT2 Others Unspecified Activity = 0.13 n.a. PMID[456644]
NPT79 Organism Bacillus subtilis Bacillus subtilis IZ = 19.0 mm PMID[456644]
NPT20 Organism Candida albicans Candida albicans IZ = 11.0 mm PMID[456644]
NPT2 Others Unspecified Activity > 25.0 n.a. PMID[456644]
NPT2 Others Unspecified Ratio IC50 > 187.0 n.a. PMID[456644]

☑ 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 NPC25340 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 NPC56796
0.9495 High Similarity NPC474583
0.8824 High Similarity NPC471083
0.87 High Similarity NPC476903
0.8571 High Similarity NPC55462
0.8286 Intermediate Similarity NPC50815
0.8257 Intermediate Similarity NPC472359
0.8113 Intermediate Similarity NPC247060
0.8037 Intermediate Similarity NPC241879
0.7961 Intermediate Similarity NPC243985
0.7961 Intermediate Similarity NPC280710
0.7925 Intermediate Similarity NPC275686
0.7909 Intermediate Similarity NPC159367
0.7905 Intermediate Similarity NPC240650
0.7788 Intermediate Similarity NPC80834
0.7788 Intermediate Similarity NPC469968
0.7706 Intermediate Similarity NPC90538
0.7658 Intermediate Similarity NPC169375
0.7642 Intermediate Similarity NPC289140
0.7568 Intermediate Similarity NPC36497
0.7563 Intermediate Similarity NPC242692
0.7547 Intermediate Similarity NPC311164
0.7547 Intermediate Similarity NPC272732
0.7545 Intermediate Similarity NPC293299
0.7545 Intermediate Similarity NPC45365
0.7525 Intermediate Similarity NPC75810
0.75 Intermediate Similarity NPC140685
0.75 Intermediate Similarity NPC91604
0.7407 Intermediate Similarity NPC140300
0.7355 Intermediate Similarity NPC472458
0.7353 Intermediate Similarity NPC152684
0.7345 Intermediate Similarity NPC46981
0.7308 Intermediate Similarity NPC34754
0.7288 Intermediate Similarity NPC165396
0.7282 Intermediate Similarity NPC166458
0.7273 Intermediate Similarity NPC135799
0.7248 Intermediate Similarity NPC474164
0.7241 Intermediate Similarity NPC474459
0.7241 Intermediate Similarity NPC66862
0.7207 Intermediate Similarity NPC118275
0.7179 Intermediate Similarity NPC474452
0.7168 Intermediate Similarity NPC119329
0.7155 Intermediate Similarity NPC72753
0.7155 Intermediate Similarity NPC328052
0.7155 Intermediate Similarity NPC472313
0.7119 Intermediate Similarity NPC478137
0.7105 Intermediate Similarity NPC86906
0.704 Intermediate Similarity NPC237286
0.7018 Intermediate Similarity NPC475239
0.7018 Intermediate Similarity NPC212874
0.6991 Remote Similarity NPC176012
0.6972 Remote Similarity NPC473314
0.697 Remote Similarity NPC189883
0.6961 Remote Similarity NPC257962
0.6957 Remote Similarity NPC258130
0.6937 Remote Similarity NPC167419
0.6881 Remote Similarity NPC93027
0.687 Remote Similarity NPC470596
0.6869 Remote Similarity NPC257347
0.6869 Remote Similarity NPC141071
0.6869 Remote Similarity NPC471723
0.6857 Remote Similarity NPC24733
0.6852 Remote Similarity NPC84171
0.6842 Remote Similarity NPC152718
0.681 Remote Similarity NPC477292
0.6807 Remote Similarity NPC79238
0.68 Remote Similarity NPC202642
0.68 Remote Similarity NPC237460
0.68 Remote Similarity NPC129165
0.68 Remote Similarity NPC300324
0.68 Remote Similarity NPC134330
0.68 Remote Similarity NPC240604
0.68 Remote Similarity NPC46160
0.6796 Remote Similarity NPC192456
0.6768 Remote Similarity NPC476904
0.6767 Remote Similarity NPC132847
0.6765 Remote Similarity NPC1319
0.6735 Remote Similarity NPC21773
0.6733 Remote Similarity NPC214570
0.6731 Remote Similarity NPC283277
0.6721 Remote Similarity NPC304646
0.6721 Remote Similarity NPC28280
0.67 Remote Similarity NPC28657
0.67 Remote Similarity NPC230301
0.67 Remote Similarity NPC22105
0.67 Remote Similarity NPC304309
0.67 Remote Similarity NPC285893
0.67 Remote Similarity NPC162742
0.67 Remote Similarity NPC118508
0.67 Remote Similarity NPC121744
0.67 Remote Similarity NPC134847
0.67 Remote Similarity NPC322353
0.67 Remote Similarity NPC288035
0.67 Remote Similarity NPC136188
0.6699 Remote Similarity NPC236112
0.6696 Remote Similarity NPC476755
0.6696 Remote Similarity NPC226509
0.6695 Remote Similarity NPC470595
0.6667 Remote Similarity NPC186191
0.6667 Remote Similarity NPC167037
0.6667 Remote Similarity NPC302041
0.6667 Remote Similarity NPC246956
0.6667 Remote Similarity NPC138621
0.6667 Remote Similarity NPC6978
0.6667 Remote Similarity NPC275910
0.6667 Remote Similarity NPC244385
0.6667 Remote Similarity NPC85346
0.6667 Remote Similarity NPC205455
0.6667 Remote Similarity NPC285761
0.6667 Remote Similarity NPC65897
0.6639 Remote Similarity NPC95920
0.6639 Remote Similarity NPC470540
0.6639 Remote Similarity NPC253645
0.6639 Remote Similarity NPC85001
0.6639 Remote Similarity NPC147835
0.6638 Remote Similarity NPC98765
0.6637 Remote Similarity NPC4834
0.6637 Remote Similarity NPC292819
0.6635 Remote Similarity NPC109533
0.6635 Remote Similarity NPC474531
0.6634 Remote Similarity NPC321381
0.6634 Remote Similarity NPC321016
0.6634 Remote Similarity NPC73875
0.6634 Remote Similarity NPC244488
0.6634 Remote Similarity NPC247325
0.6634 Remote Similarity NPC470362
0.6634 Remote Similarity NPC107059
0.6634 Remote Similarity NPC113733
0.6634 Remote Similarity NPC7214
0.6602 Remote Similarity NPC209430
0.6602 Remote Similarity NPC30986
0.6602 Remote Similarity NPC273410
0.6602 Remote Similarity NPC80530
0.6581 Remote Similarity NPC469958
0.6571 Remote Similarity NPC215474
0.6571 Remote Similarity NPC224072
0.6571 Remote Similarity NPC39966
0.6571 Remote Similarity NPC30166
0.6571 Remote Similarity NPC470049
0.6569 Remote Similarity NPC198968
0.6569 Remote Similarity NPC34019
0.6569 Remote Similarity NPC318495
0.6569 Remote Similarity NPC155986
0.6538 Remote Similarity NPC322313
0.6538 Remote Similarity NPC236237
0.6538 Remote Similarity NPC13554
0.6538 Remote Similarity NPC102253
0.6535 Remote Similarity NPC478138
0.6525 Remote Similarity NPC195841
0.6525 Remote Similarity NPC233256
0.6514 Remote Similarity NPC324405
0.6505 Remote Similarity NPC87604
0.6505 Remote Similarity NPC477514
0.6505 Remote Similarity NPC474216
0.6505 Remote Similarity NPC312328
0.6505 Remote Similarity NPC76931
0.6505 Remote Similarity NPC307965
0.6505 Remote Similarity NPC18603
0.6505 Remote Similarity NPC477522
0.6505 Remote Similarity NPC473943
0.6505 Remote Similarity NPC318136
0.65 Remote Similarity NPC474140
0.65 Remote Similarity NPC201373
0.65 Remote Similarity NPC182717
0.6496 Remote Similarity NPC473254
0.6476 Remote Similarity NPC470383
0.6475 Remote Similarity NPC476498
0.6475 Remote Similarity NPC124358
0.6449 Remote Similarity NPC124172
0.6449 Remote Similarity NPC209802
0.6449 Remote Similarity NPC478102
0.6449 Remote Similarity NPC470077
0.6446 Remote Similarity NPC287764
0.6442 Remote Similarity NPC109546
0.6442 Remote Similarity NPC328714
0.6442 Remote Similarity NPC81306
0.6442 Remote Similarity NPC84694
0.6442 Remote Similarity NPC47982
0.6442 Remote Similarity NPC28862
0.6442 Remote Similarity NPC143182
0.6436 Remote Similarity NPC100334
0.6436 Remote Similarity NPC469533
0.6436 Remote Similarity NPC469593
0.6436 Remote Similarity NPC469534
0.6429 Remote Similarity NPC35037
0.6429 Remote Similarity NPC160209
0.6415 Remote Similarity NPC202389
0.6415 Remote Similarity NPC218616
0.6415 Remote Similarity NPC296701
0.6415 Remote Similarity NPC101462
0.6415 Remote Similarity NPC87489
0.6415 Remote Similarity NPC49964
0.6415 Remote Similarity NPC20853
0.6415 Remote Similarity NPC201852
0.6415 Remote Similarity NPC248886
0.6406 Remote Similarity NPC469943
0.64 Remote Similarity NPC265789
0.64 Remote Similarity NPC111234
0.6389 Remote Similarity NPC318390
0.6387 Remote Similarity NPC230677

  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 NPC25340 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
0.729 Intermediate Similarity NPD5771 Approved
0.67 Remote Similarity NPD6942 Approved
0.67 Remote Similarity NPD7339 Approved
0.6667 Remote Similarity NPD4722 Approved
0.6667 Remote Similarity NPD4723 Approved
0.6538 Remote Similarity NPD7525 Registered
0.6423 Remote Similarity NPD8298 Phase 2
0.632 Remote Similarity NPD7755 Approved
0.632 Remote Similarity NPD7754 Approved
0.6311 Remote Similarity NPD3701 Clinical (unspecified phase)
0.63 Remote Similarity NPD6938 Clinical (unspecified phase)
0.63 Remote Similarity NPD6939 Phase 2
0.6299 Remote Similarity NPD7522 Discontinued
0.6239 Remote Similarity NPD8418 Phase 2
0.6238 Remote Similarity NPD4243 Approved
0.6228 Remote Similarity NPD5769 Clinical (unspecified phase)
0.621 Remote Similarity NPD7335 Phase 2
0.621 Remote Similarity NPD7337 Clinical (unspecified phase)
0.621 Remote Similarity NPD7336 Phase 2
0.6179 Remote Similarity NPD6420 Discontinued
0.6161 Remote Similarity NPD5328 Approved
0.6147 Remote Similarity NPD4786 Approved
0.6132 Remote Similarity NPD7645 Phase 2
0.6117 Remote Similarity NPD6926 Approved
0.6117 Remote Similarity NPD4785 Approved
0.6117 Remote Similarity NPD6924 Approved
0.6117 Remote Similarity NPD4784 Approved
0.6087 Remote Similarity NPD5707 Approved
0.6077 Remote Similarity NPD6908 Approved
0.6077 Remote Similarity NPD6909 Approved
0.6068 Remote Similarity NPD7919 Phase 3
0.6068 Remote Similarity NPD7920 Phase 3
0.6053 Remote Similarity NPD6079 Approved
0.604 Remote Similarity NPD6923 Approved
0.604 Remote Similarity NPD6922 Approved
0.6036 Remote Similarity NPD3618 Phase 1
0.6017 Remote Similarity NPD8088 Phase 1
0.6 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6 Remote Similarity NPD6933 Approved
0.5984 Remote Similarity NPD6920 Discontinued
0.5984 Remote Similarity NPD7333 Discontinued
0.598 Remote Similarity NPD7143 Approved
0.598 Remote Similarity NPD7144 Approved
0.5966 Remote Similarity NPD6404 Discontinued
0.5965 Remote Similarity NPD4001 Clinical (unspecified phase)
0.5963 Remote Similarity NPD3667 Approved
0.5941 Remote Similarity NPD6705 Phase 1
0.5935 Remote Similarity NPD7646 Clinical (unspecified phase)
0.5922 Remote Similarity NPD7151 Approved
0.5922 Remote Similarity NPD7152 Approved
0.5922 Remote Similarity NPD7150 Approved
0.5905 Remote Similarity NPD5275 Approved
0.5905 Remote Similarity NPD4190 Phase 3
0.5887 Remote Similarity NPD6334 Approved
0.5887 Remote Similarity NPD6415 Discontinued
0.5887 Remote Similarity NPD6333 Approved
0.5862 Remote Similarity NPD4202 Approved
0.5856 Remote Similarity NPD3665 Phase 1
0.5856 Remote Similarity NPD3666 Approved
0.5856 Remote Similarity NPD3133 Approved
0.5849 Remote Similarity NPD1346 Approved
0.5847 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5841 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5839 Remote Similarity NPD6914 Discontinued
0.5833 Remote Similarity NPD6929 Approved
0.5827 Remote Similarity NPD8077 Approved
0.5827 Remote Similarity NPD8078 Approved
0.5826 Remote Similarity NPD6700 Approved
0.5826 Remote Similarity NPD6701 Clinical (unspecified phase)
0.578 Remote Similarity NPD6930 Phase 2
0.578 Remote Similarity NPD6931 Approved
0.578 Remote Similarity NPD4748 Discontinued
0.578 Remote Similarity NPD7509 Discontinued
0.576 Remote Similarity NPD8174 Phase 2
0.5726 Remote Similarity NPD6640 Phase 3
0.5726 Remote Similarity NPD5357 Phase 1
0.5714 Remote Similarity NPD5220 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5222 Approved
0.5714 Remote Similarity NPD5221 Approved
0.5714 Remote Similarity NPD4697 Phase 3
0.5688 Remote Similarity NPD4195 Approved
0.5667 Remote Similarity NPD4755 Approved
0.5667 Remote Similarity NPD5173 Approved
0.5664 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5648 Remote Similarity NPD6932 Approved
0.5648 Remote Similarity NPD6925 Approved
0.5648 Remote Similarity NPD5776 Phase 2
0.5643 Remote Similarity NPD8449 Approved
0.5641 Remote Similarity NPD6703 Approved
0.5641 Remote Similarity NPD6702 Approved
0.5625 Remote Similarity NPD6695 Phase 3
0.5614 Remote Similarity NPD5279 Phase 3
0.5603 Remote Similarity NPD4753 Phase 2
0.5603 Remote Similarity NPD8450 Suspended

  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