Structure

Physi-Chem Properties

Molecular Weight:  398.37
Volume:  452.123
LogP:  5.982
LogD:  4.967
LogS:  -5.296
# Rotatable Bonds:  2
TPSA:  38.05
# H-Bond Aceptor:  2
# H-Bond Donor:  3
# Rings:  5
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.567
Synthetic Accessibility Score:  4.783
Fsp3:  0.926
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:  -5.355
MDCK Permeability:  4.398965756990947e-06
Pgp-inhibitor:  0.116
Pgp-substrate:  0.962
Human Intestinal Absorption (HIA):  0.071
20% Bioavailability (F20%):  0.918
30% Bioavailability (F30%):  0.153

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.242
Plasma Protein Binding (PPB):  72.19695281982422%
Volume Distribution (VD):  0.581
Pgp-substrate:  7.088116645812988%

ADMET: Metabolism

CYP1A2-inhibitor:  0.177
CYP1A2-substrate:  0.2
CYP2C19-inhibitor:  0.152
CYP2C19-substrate:  0.823
CYP2C9-inhibitor:  0.092
CYP2C9-substrate:  0.02
CYP2D6-inhibitor:  0.977
CYP2D6-substrate:  0.904
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.325

ADMET: Excretion

Clearance (CL):  13.068
Half-life (T1/2):  0.022

ADMET: Toxicity

hERG Blockers:  0.993
Human Hepatotoxicity (H-HT):  0.461
Drug-inuced Liver Injury (DILI):  0.797
AMES Toxicity:  0.103
Rat Oral Acute Toxicity:  0.619
Maximum Recommended Daily Dose:  0.903
Skin Sensitization:  0.962
Carcinogencity:  0.372
Eye Corrosion:  0.476
Eye Irritation:  0.011
Respiratory Toxicity:  0.901

Download Data

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

  Natural Product: NPC12035

Natural Product ID:  NPC12035
Common Name*:   3Beta-Amino-22,26-Epiminocholest-5-Ene Named Sarachine
IUPAC Name:   (3S,8S,9S,10R,13S,14S,17R)-10,13-dimethyl-17-[(1S)-1-[(2R,5S)-5-methylpiperidin-2-yl]ethyl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-amine
Synonyms:  
Standard InCHIKey:  DHMOPSVHROLSFF-OWJFKGPJSA-N
Standard InCHI:  InChI=1S/C27H46N2/c1-17-5-10-25(29-16-17)18(2)22-8-9-23-21-7-6-19-15-20(28)11-13-26(19,3)24(21)12-14-27(22,23)4/h6,17-18,20-25,29H,5,7-16,28H2,1-4H3/t17-,18-,20-,21-,22+,23-,24-,25+,26-,27+/m0/s1
SMILES:  C[C@H]1CC[C@H]([C@@H](C)[C@H]2CC[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)N)NC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464561
PubChem CID:   10668589
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0002724] Steroidal alkaloids
          • [CHEMONTID:0002732] 22,26-epiminocholestanes
            • [CHEMONTID:0002736] 3-amino-22,26-epiminocholestanes

*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
NPO3141 Saracha punctata Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[9834160]
NPO3141 Saracha punctata Species Solanaceae 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
NPT91 Cell Line KB Homo sapiens IC50 = 50000.0 nM PMID[523021]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Inhibition = 100.0 % PMID[523021]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Inhibition = 50.0 % PMID[523021]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi Inhibition = 0.0 % PMID[523021]
NPT1208 Organism Leishmania braziliensis Leishmania braziliensis Inhibition = 100.0 % PMID[523021]
NPT1208 Organism Leishmania braziliensis Leishmania braziliensis Inhibition = 50.0 % PMID[523021]
NPT1208 Organism Leishmania braziliensis Leishmania braziliensis Inhibition = 0.0 % PMID[523021]
NPT1219 Organism Leishmania chagasi Leishmania chagasi Inhibition = 100.0 % PMID[523021]
NPT1219 Organism Leishmania chagasi Leishmania chagasi Inhibition = 50.0 % PMID[523021]
NPT1219 Organism Leishmania chagasi Leishmania chagasi Inhibition = 0.0 % PMID[523021]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis Inhibition = 100.0 % PMID[523021]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis Inhibition = 50.0 % PMID[523021]
NPT634 Organism Leishmania amazonensis Leishmania amazonensis Inhibition = 0.0 % PMID[523021]
NPT27 Others Unspecified Activity = 0.0 % PMID[523021]
NPT27 Others Unspecified Activity = 95.0 % PMID[523021]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 25.0 nM PMID[523021]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 176.0 nM PMID[523021]
NPT2 Others Unspecified Ratio IC50 = 2000.0 n.a. PMID[523021]
NPT2 Others Unspecified Ratio IC50 = 286.0 n.a. PMID[523021]
NPT474 Organism Plasmodium berghei Plasmodium berghei Activity = 69.0 % PMID[523021]
NPT474 Organism Plasmodium berghei Plasmodium berghei Activity = 27.0 % PMID[523021]
NPT474 Organism Plasmodium berghei Plasmodium berghei Activity = 16.0 % PMID[523021]

☑ 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 NPC12035 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
0.9103 High Similarity NPC329782
0.9103 High Similarity NPC118329
0.9103 High Similarity NPC152039
0.8987 High Similarity NPC472312
0.8667 High Similarity NPC21773
0.8608 High Similarity NPC211322
0.8462 Intermediate Similarity NPC7214
0.8442 Intermediate Similarity NPC476904
0.8434 Intermediate Similarity NPC24733
0.8415 Intermediate Similarity NPC171639
0.8395 Intermediate Similarity NPC474122
0.8182 Intermediate Similarity NPC265789
0.8072 Intermediate Similarity NPC283277
0.7857 Intermediate Similarity NPC215474
0.7826 Intermediate Similarity NPC474164
0.7654 Intermediate Similarity NPC125828
0.7561 Intermediate Similarity NPC259989
0.7561 Intermediate Similarity NPC174803
0.7558 Intermediate Similarity NPC21667
0.75 Intermediate Similarity NPC58200
0.75 Intermediate Similarity NPC176012
0.7416 Intermediate Similarity NPC43308
0.7403 Intermediate Similarity NPC469970
0.7368 Intermediate Similarity NPC472544
0.7363 Intermediate Similarity NPC84171
0.7273 Intermediate Similarity NPC53276
0.7191 Intermediate Similarity NPC147513
0.7128 Intermediate Similarity NPC476754
0.7125 Intermediate Similarity NPC271640
0.7111 Intermediate Similarity NPC157479
0.7079 Intermediate Similarity NPC471867
0.7021 Intermediate Similarity NPC476752
0.7021 Intermediate Similarity NPC476753
0.7 Intermediate Similarity NPC75810
0.7 Intermediate Similarity NPC152684
0.6961 Remote Similarity NPC159367
0.6939 Remote Similarity NPC135799
0.6931 Remote Similarity NPC230677
0.6923 Remote Similarity NPC166458
0.6907 Remote Similarity NPC167419
0.6893 Remote Similarity NPC85001
0.6893 Remote Similarity NPC147835
0.6893 Remote Similarity NPC253645
0.6893 Remote Similarity NPC95920
0.6837 Remote Similarity NPC91604
0.6827 Remote Similarity NPC472313
0.6795 Remote Similarity NPC219621
0.6765 Remote Similarity NPC233256
0.6765 Remote Similarity NPC195841
0.6762 Remote Similarity NPC79238
0.6762 Remote Similarity NPC474459
0.6753 Remote Similarity NPC21781
0.6744 Remote Similarity NPC25110
0.6742 Remote Similarity NPC90150
0.6705 Remote Similarity NPC57599
0.67 Remote Similarity NPC118275
0.6698 Remote Similarity NPC474452
0.6633 Remote Similarity NPC476903
0.663 Remote Similarity NPC182106
0.663 Remote Similarity NPC311769
0.6627 Remote Similarity NPC184919
0.6627 Remote Similarity NPC138409
0.6623 Remote Similarity NPC472830
0.6559 Remote Similarity NPC56107
0.6556 Remote Similarity NPC257962
0.6552 Remote Similarity NPC476308
0.6535 Remote Similarity NPC474582
0.6522 Remote Similarity NPC116881
0.6522 Remote Similarity NPC57163
0.6514 Remote Similarity NPC28280
0.6514 Remote Similarity NPC304646
0.65 Remote Similarity NPC140685
0.6465 Remote Similarity NPC289140
0.6463 Remote Similarity NPC37792
0.6456 Remote Similarity NPC317778
0.6447 Remote Similarity NPC123194
0.6421 Remote Similarity NPC259252
0.6415 Remote Similarity NPC175585
0.641 Remote Similarity NPC469769
0.641 Remote Similarity NPC231129
0.6381 Remote Similarity NPC46981
0.6354 Remote Similarity NPC249312
0.6346 Remote Similarity NPC212874
0.6329 Remote Similarity NPC474454
0.6329 Remote Similarity NPC472827
0.6329 Remote Similarity NPC474420
0.6329 Remote Similarity NPC82919
0.6329 Remote Similarity NPC474455
0.6327 Remote Similarity NPC93027
0.6311 Remote Similarity NPC471083
0.6311 Remote Similarity NPC152718
0.6296 Remote Similarity NPC474086
0.6286 Remote Similarity NPC474695
0.6286 Remote Similarity NPC86906
0.6282 Remote Similarity NPC474415
0.6282 Remote Similarity NPC475696
0.6282 Remote Similarity NPC474528
0.6275 Remote Similarity NPC239768
0.6275 Remote Similarity NPC128698
0.625 Remote Similarity NPC311809
0.625 Remote Similarity NPC98765
0.6234 Remote Similarity NPC469770
0.622 Remote Similarity NPC476559
0.6207 Remote Similarity NPC296686
0.6203 Remote Similarity NPC324944
0.62 Remote Similarity NPC311164
0.62 Remote Similarity NPC272732
0.6184 Remote Similarity NPC127944
0.6174 Remote Similarity NPC478138
0.6163 Remote Similarity NPC473442
0.6163 Remote Similarity NPC120167
0.6154 Remote Similarity NPC50815
0.6154 Remote Similarity NPC226509
0.6125 Remote Similarity NPC475716
0.6117 Remote Similarity NPC275686
0.61 Remote Similarity NPC280710
0.61 Remote Similarity NPC243985
0.6098 Remote Similarity NPC145715
0.6095 Remote Similarity NPC241879
0.6092 Remote Similarity NPC476329
0.6081 Remote Similarity NPC22765
0.6081 Remote Similarity NPC17518
0.6078 Remote Similarity NPC184033
0.6078 Remote Similarity NPC140300
0.6076 Remote Similarity NPC474457
0.6076 Remote Similarity NPC470369
0.6076 Remote Similarity NPC173815
0.6076 Remote Similarity NPC470370
0.6075 Remote Similarity NPC25340
0.6064 Remote Similarity NPC153734
0.6058 Remote Similarity NPC474001
0.6058 Remote Similarity NPC34193
0.6053 Remote Similarity NPC35037
0.6047 Remote Similarity NPC124384
0.6047 Remote Similarity NPC245223
0.6038 Remote Similarity NPC469958
0.6038 Remote Similarity NPC475239
0.6036 Remote Similarity NPC478137
0.6024 Remote Similarity NPC473959
0.6 Remote Similarity NPC247060
0.6 Remote Similarity NPC176107
0.5981 Remote Similarity NPC477292
0.5977 Remote Similarity NPC472543
0.5974 Remote Similarity NPC472828
0.5966 Remote Similarity NPC317654
0.5966 Remote Similarity NPC96010
0.5957 Remote Similarity NPC471868
0.5949 Remote Similarity NPC318036
0.5946 Remote Similarity NPC124358
0.5943 Remote Similarity NPC90538
0.5943 Remote Similarity NPC474583
0.593 Remote Similarity NPC20610
0.5926 Remote Similarity NPC476756
0.5926 Remote Similarity NPC244982
0.5922 Remote Similarity NPC240650
0.5917 Remote Similarity NPC478136
0.5909 Remote Similarity NPC110615
0.5902 Remote Similarity NPC40488
0.5882 Remote Similarity NPC476261
0.5882 Remote Similarity NPC470382
0.5882 Remote Similarity NPC25033
0.5882 Remote Similarity NPC474456
0.5882 Remote Similarity NPC471635
0.5882 Remote Similarity NPC119225
0.5882 Remote Similarity NPC92327
0.5872 Remote Similarity NPC24596
0.587 Remote Similarity NPC39308
0.5862 Remote Similarity NPC182815
0.5862 Remote Similarity NPC472831
0.5833 Remote Similarity NPC55462
0.5823 Remote Similarity NPC470893
0.5816 Remote Similarity NPC21035
0.5804 Remote Similarity NPC56796
0.5795 Remote Similarity NPC35734
0.5795 Remote Similarity NPC159577
0.5795 Remote Similarity NPC282593
0.5795 Remote Similarity NPC475728
0.5789 Remote Similarity NPC201713
0.5789 Remote Similarity NPC200129
0.5789 Remote Similarity NPC246904
0.5778 Remote Similarity NPC17770
0.5772 Remote Similarity NPC25455
0.5772 Remote Similarity NPC15249
0.5766 Remote Similarity NPC72753
0.5741 Remote Similarity NPC119329
0.5739 Remote Similarity NPC473573
0.5733 Remote Similarity NPC124851
0.5732 Remote Similarity NPC28755
0.5732 Remote Similarity NPC152211
0.573 Remote Similarity NPC115023
0.573 Remote Similarity NPC470078
0.5729 Remote Similarity NPC161344
0.5728 Remote Similarity NPC174117
0.5728 Remote Similarity NPC329430
0.5726 Remote Similarity NPC122819
0.5714 Remote Similarity NPC66862
0.5714 Remote Similarity NPC293803
0.57 Remote Similarity NPC323156
0.5688 Remote Similarity NPC185929
0.568 Remote Similarity NPC150057

  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 NPC12035 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
0.7722 Intermediate Similarity NPD5365 Phase 2
0.6548 Remote Similarity NPD6939 Phase 2
0.6548 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6486 Remote Similarity NPD3721 Approved
0.6486 Remote Similarity NPD3722 Approved
0.6389 Remote Similarity NPD7336 Phase 2
0.6389 Remote Similarity NPD7337 Clinical (unspecified phase)
0.6389 Remote Similarity NPD7335 Phase 2
0.61 Remote Similarity NPD3982 Approved
0.61 Remote Similarity NPD3980 Approved
0.5941 Remote Similarity NPD5771 Approved
0.5941 Remote Similarity NPD2878 Approved
0.59 Remote Similarity NPD4543 Discontinued
0.5897 Remote Similarity NPD3727 Discontinued
0.5825 Remote Similarity NPD1738 Approved
0.5816 Remote Similarity NPD4145 Approved
0.5816 Remote Similarity NPD4146 Approved
0.5806 Remote Similarity NPD7155 Clinical (unspecified phase)
0.58 Remote Similarity NPD5915 Approved
0.5784 Remote Similarity NPD5769 Clinical (unspecified phase)
0.5769 Remote Similarity NPD713 Clinical (unspecified phase)
0.573 Remote Similarity NPD4243 Approved
0.5726 Remote Similarity NPD8449 Approved
0.568 Remote Similarity NPD8450 Suspended
0.5673 Remote Similarity NPD5963 Phase 2
0.5673 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5673 Remote Similarity NPD2005 Discontinued
0.5673 Remote Similarity NPD5964 Phase 2
0.566 Remote Similarity NPD1946 Clinical (unspecified phase)
0.5618 Remote Similarity NPD4747 Approved
0.5604 Remote Similarity NPD4784 Approved
0.5604 Remote Similarity NPD4785 Approved
0.56 Remote Similarity NPD874 Approved
0.56 Remote Similarity NPD872 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