Structure

Physi-Chem Properties

Molecular Weight:  329.18
Volume:  326.645
LogP:  0.447
LogD:  0.897
LogS:  -1.41
# Rotatable Bonds:  7
TPSA:  99.46
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.444
Synthetic Accessibility Score:  4.535
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.947
MDCK Permeability:  0.0001245645253220573
Pgp-inhibitor:  0.003
Pgp-substrate:  0.213
Human Intestinal Absorption (HIA):  0.073
20% Bioavailability (F20%):  0.434
30% Bioavailability (F30%):  0.566

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.227
Plasma Protein Binding (PPB):  21.700471878051758%
Volume Distribution (VD):  0.542
Pgp-substrate:  79.75067138671875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.083
CYP2C19-inhibitor:  0.012
CYP2C19-substrate:  0.676
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.2
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.26

ADMET: Excretion

Clearance (CL):  3.269
Half-life (T1/2):  0.655

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.107
Drug-inuced Liver Injury (DILI):  0.229
AMES Toxicity:  0.793
Rat Oral Acute Toxicity:  0.039
Maximum Recommended Daily Dose:  0.245
Skin Sensitization:  0.085
Carcinogencity:  0.964
Eye Corrosion:  0.004
Eye Irritation:  0.019
Respiratory Toxicity:  0.879

Download Data

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

  Natural Product: NPC6271

Natural Product ID:  NPC6271
Common Name*:   Europine
IUPAC Name:   [(7S,8R)-7-hydroxy-5,6,7,8-tetrahydro-3H-pyrrolizin-1-yl]methyl (2R)-2,3-dihydroxy-2-[(1S)-1-methoxyethyl]-3-methylbutanoate
Synonyms:   Europine
Standard InCHIKey:  ZNEMYFCJOCCUJN-VFFTVRQLSA-N
Standard InCHI:  InChI=1S/C16H27NO6/c1-10(22-4)16(21,15(2,3)20)14(19)23-9-11-5-7-17-8-6-12(18)13(11)17/h5,10,12-13,18,20-21H,6-9H2,1-4H3/t10-,12-,13+,16-/m0/s1
SMILES:  CO[C@H]([C@@](C(O)(C)C)(C(=O)OCC1=CCN2[C@H]1[C@@H](O)CC2)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL526357
PubChem CID:   5462451
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives

*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
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20494 Heliotropium rotundifolium Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20494 Heliotropium rotundifolium Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO149 Heliotropium europaeum Species Heliotropiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20494 Heliotropium rotundifolium Species Heliotropiaceae 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
NPT776 Organism Spodoptera littoralis Spodoptera littoralis Activity = 67.0 % PMID[480178]

☑ 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 NPC6271 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
0.9896 High Similarity NPC64168
0.9792 High Similarity NPC80439
0.9792 High Similarity NPC279833
0.9792 High Similarity NPC173690
0.9126 High Similarity NPC316984
0.9126 High Similarity NPC30911
0.8796 High Similarity NPC201889
0.8796 High Similarity NPC106791
0.8426 Intermediate Similarity NPC130124
0.8426 Intermediate Similarity NPC193471
0.8393 Intermediate Similarity NPC23963
0.8241 Intermediate Similarity NPC168758
0.8241 Intermediate Similarity NPC47857
0.8241 Intermediate Similarity NPC181510
0.8125 Intermediate Similarity NPC284656
0.7807 Intermediate Similarity NPC235625
0.7522 Intermediate Similarity NPC275100
0.7368 Intermediate Similarity NPC474497
0.7345 Intermediate Similarity NPC195435
0.7345 Intermediate Similarity NPC196073
0.7255 Intermediate Similarity NPC52533
0.7182 Intermediate Similarity NPC473289
0.708 Intermediate Similarity NPC271562
0.7059 Intermediate Similarity NPC200412
0.7059 Intermediate Similarity NPC156336
0.7059 Intermediate Similarity NPC120599
0.7027 Intermediate Similarity NPC474244
0.7009 Intermediate Similarity NPC469597
0.6972 Remote Similarity NPC52820
0.6937 Remote Similarity NPC188785
0.687 Remote Similarity NPC474099
0.6838 Remote Similarity NPC474411
0.6838 Remote Similarity NPC474431
0.6814 Remote Similarity NPC474828
0.6814 Remote Similarity NPC68001
0.6814 Remote Similarity NPC474827
0.6814 Remote Similarity NPC199831
0.68 Remote Similarity NPC474371
0.6754 Remote Similarity NPC469604
0.6696 Remote Similarity NPC93179
0.6693 Remote Similarity NPC471086
0.6667 Remote Similarity NPC469860
0.6667 Remote Similarity NPC130436
0.6667 Remote Similarity NPC469861
0.6667 Remote Similarity NPC11379
0.6636 Remote Similarity NPC150041
0.6634 Remote Similarity NPC99651
0.661 Remote Similarity NPC469603
0.6609 Remote Similarity NPC44514
0.6589 Remote Similarity NPC477988
0.6587 Remote Similarity NPC477985
0.6587 Remote Similarity NPC326386
0.6587 Remote Similarity NPC471087
0.6585 Remote Similarity NPC471261
0.6557 Remote Similarity NPC65045
0.6532 Remote Similarity NPC230849
0.6529 Remote Similarity NPC472536
0.6529 Remote Similarity NPC103391
0.6518 Remote Similarity NPC476344
0.6514 Remote Similarity NPC299808
0.6514 Remote Similarity NPC72183
0.6514 Remote Similarity NPC118844
0.6514 Remote Similarity NPC110875
0.6489 Remote Similarity NPC133089
0.6475 Remote Similarity NPC30196
0.6471 Remote Similarity NPC113012
0.6471 Remote Similarity NPC122926
0.6462 Remote Similarity NPC215507
0.6439 Remote Similarity NPC120420
0.6436 Remote Similarity NPC474278
0.6436 Remote Similarity NPC233108
0.6423 Remote Similarity NPC6531
0.6417 Remote Similarity NPC58281
0.6412 Remote Similarity NPC120335
0.6406 Remote Similarity NPC329401
0.6406 Remote Similarity NPC477987
0.6391 Remote Similarity NPC99864
0.6391 Remote Similarity NPC471256
0.6389 Remote Similarity NPC476803
0.6389 Remote Similarity NPC287089
0.6379 Remote Similarity NPC471260
0.6378 Remote Similarity NPC293550
0.6378 Remote Similarity NPC477990
0.6378 Remote Similarity NPC323168
0.6378 Remote Similarity NPC111162
0.6378 Remote Similarity NPC471255
0.6378 Remote Similarity NPC318445
0.6378 Remote Similarity NPC477989
0.6378 Remote Similarity NPC316133
0.6372 Remote Similarity NPC241426
0.6371 Remote Similarity NPC174463
0.6364 Remote Similarity NPC1111
0.6364 Remote Similarity NPC261750
0.6357 Remote Similarity NPC314282
0.6355 Remote Similarity NPC469910
0.6355 Remote Similarity NPC478112
0.6349 Remote Similarity NPC470000
0.6348 Remote Similarity NPC185141
0.6348 Remote Similarity NPC133907
0.6348 Remote Similarity NPC110443
0.6348 Remote Similarity NPC46998
0.6348 Remote Similarity NPC128733
0.6325 Remote Similarity NPC75523
0.6316 Remote Similarity NPC471144
0.6311 Remote Similarity NPC475210
0.6306 Remote Similarity NPC469645
0.6306 Remote Similarity NPC469692
0.6286 Remote Similarity NPC474252
0.6281 Remote Similarity NPC476875
0.6279 Remote Similarity NPC471263
0.6273 Remote Similarity NPC474232
0.6271 Remote Similarity NPC471259
0.6261 Remote Similarity NPC26597
0.6261 Remote Similarity NPC475949
0.625 Remote Similarity NPC121825
0.6239 Remote Similarity NPC475945
0.6239 Remote Similarity NPC4620
0.6239 Remote Similarity NPC475871
0.623 Remote Similarity NPC43648
0.623 Remote Similarity NPC478024
0.623 Remote Similarity NPC314550
0.623 Remote Similarity NPC60432
0.6228 Remote Similarity NPC4834
0.6228 Remote Similarity NPC218064
0.6228 Remote Similarity NPC167380
0.6216 Remote Similarity NPC9447
0.6212 Remote Similarity NPC307165
0.6207 Remote Similarity NPC472753
0.6204 Remote Similarity NPC278283
0.6202 Remote Similarity NPC313333
0.6202 Remote Similarity NPC314451
0.6202 Remote Similarity NPC313342
0.6202 Remote Similarity NPC314512
0.6186 Remote Similarity NPC220964
0.6186 Remote Similarity NPC475676
0.6183 Remote Similarity NPC329919
0.6183 Remote Similarity NPC477793
0.6172 Remote Similarity NPC471262
0.6168 Remote Similarity NPC158756
0.6165 Remote Similarity NPC316401
0.6154 Remote Similarity NPC472754
0.6154 Remote Similarity NPC471148
0.6154 Remote Similarity NPC474747
0.6154 Remote Similarity NPC471258
0.6148 Remote Similarity NPC29501
0.6147 Remote Similarity NPC266957
0.614 Remote Similarity NPC473333
0.614 Remote Similarity NPC121857
0.6139 Remote Similarity NPC474280
0.6139 Remote Similarity NPC473489
0.6132 Remote Similarity NPC475046
0.6132 Remote Similarity NPC11383
0.6132 Remote Similarity NPC474959
0.6132 Remote Similarity NPC310450
0.6126 Remote Similarity NPC316228
0.6116 Remote Similarity NPC38154
0.6111 Remote Similarity NPC471156
0.6111 Remote Similarity NPC470755
0.6107 Remote Similarity NPC476951
0.6106 Remote Similarity NPC469632
0.6102 Remote Similarity NPC472755
0.6102 Remote Similarity NPC265094
0.6098 Remote Similarity NPC474995
0.6098 Remote Similarity NPC276995
0.6098 Remote Similarity NPC279383
0.6098 Remote Similarity NPC76660
0.6091 Remote Similarity NPC476805
0.6087 Remote Similarity NPC2666
0.6087 Remote Similarity NPC471490
0.6083 Remote Similarity NPC324327
0.6083 Remote Similarity NPC72813
0.6083 Remote Similarity NPC326994
0.6083 Remote Similarity NPC474421
0.6083 Remote Similarity NPC26617
0.6083 Remote Similarity NPC194620
0.6078 Remote Similarity NPC329852
0.6078 Remote Similarity NPC473582
0.6075 Remote Similarity NPC286770
0.6075 Remote Similarity NPC161045
0.6075 Remote Similarity NPC229799
0.6075 Remote Similarity NPC284472
0.6068 Remote Similarity NPC474742
0.6068 Remote Similarity NPC474339
0.6068 Remote Similarity NPC474873
0.6068 Remote Similarity NPC164598
0.6063 Remote Similarity NPC477986
0.6063 Remote Similarity NPC138534
0.6058 Remote Similarity NPC279532
0.6055 Remote Similarity NPC258824
0.6055 Remote Similarity NPC469483
0.6055 Remote Similarity NPC261721
0.6053 Remote Similarity NPC471492
0.605 Remote Similarity NPC474741
0.605 Remote Similarity NPC472756
0.605 Remote Similarity NPC205176
0.6048 Remote Similarity NPC475988
0.6038 Remote Similarity NPC474894
0.6038 Remote Similarity NPC52861
0.6036 Remote Similarity NPC473564
0.6036 Remote Similarity NPC130359

  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 NPC6271 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
0.9126 High Similarity NPD2204 Approved
0.648 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6423 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6406 Remote Similarity NPD8273 Phase 1
0.6406 Remote Similarity NPD8451 Approved
0.6391 Remote Similarity NPD8415 Approved
0.6378 Remote Similarity NPD7642 Approved
0.6357 Remote Similarity NPD2575 Approved
0.6357 Remote Similarity NPD8448 Approved
0.6343 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6299 Remote Similarity NPD8080 Discontinued
0.6212 Remote Similarity NPD8391 Approved
0.6212 Remote Similarity NPD8390 Approved
0.6212 Remote Similarity NPD8392 Approved
0.6202 Remote Similarity NPD8341 Approved
0.6202 Remote Similarity NPD8340 Approved
0.6202 Remote Similarity NPD8342 Approved
0.6202 Remote Similarity NPD8299 Approved
0.6179 Remote Similarity NPD1376 Discontinued
0.614 Remote Similarity NPD4228 Discovery
0.6083 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6045 Remote Similarity NPD3662 Phase 3
0.6045 Remote Similarity NPD3663 Approved
0.6045 Remote Similarity NPD3664 Approved
0.6045 Remote Similarity NPD3661 Approved
0.6015 Remote Similarity NPD2627 Approved
0.6015 Remote Similarity NPD2625 Approved
0.6015 Remote Similarity NPD2160 Approved
0.6015 Remote Similarity NPD2628 Approved
0.6015 Remote Similarity NPD2626 Approved
0.6015 Remote Similarity NPD2159 Approved
0.6 Remote Similarity NPD8384 Approved
0.6 Remote Similarity NPD2613 Approved
0.5984 Remote Similarity NPD7641 Discontinued
0.5935 Remote Similarity NPD6421 Discontinued
0.5926 Remote Similarity NPD5204 Approved
0.5912 Remote Similarity NPD4619 Approved
0.5912 Remote Similarity NPD4621 Approved
0.5897 Remote Similarity NPD4225 Approved
0.5877 Remote Similarity NPD5781 Clinical (unspecified phase)
0.587 Remote Similarity NPD2566 Approved
0.587 Remote Similarity NPD3088 Approved
0.587 Remote Similarity NPD3089 Approved
0.587 Remote Similarity NPD3087 Approved
0.587 Remote Similarity NPD3614 Approved
0.587 Remote Similarity NPD4746 Phase 3
0.587 Remote Similarity NPD2572 Clinical (unspecified phase)
0.587 Remote Similarity NPD2574 Discontinued
0.587 Remote Similarity NPD3615 Approved
0.587 Remote Similarity NPD3090 Approved
0.587 Remote Similarity NPD3616 Approved
0.587 Remote Similarity NPD4745 Approved
0.587 Remote Similarity NPD2573 Approved
0.587 Remote Similarity NPD2571 Approved
0.587 Remote Similarity NPD2570 Approved
0.5868 Remote Similarity NPD777 Phase 3
0.5859 Remote Similarity NPD1773 Discontinued
0.5846 Remote Similarity NPD8444 Approved
0.5833 Remote Similarity NPD2611 Approved
0.5833 Remote Similarity NPD2612 Approved
0.5833 Remote Similarity NPD4217 Approved
0.5833 Remote Similarity NPD4218 Approved
0.5833 Remote Similarity NPD4216 Approved
0.5833 Remote Similarity NPD4215 Approved
0.5833 Remote Similarity NPD883 Phase 2
0.5833 Remote Similarity NPD2610 Approved
0.5833 Remote Similarity NPD2608 Approved
0.5833 Remote Similarity NPD882 Phase 2
0.5833 Remote Similarity NPD3132 Approved
0.5833 Remote Similarity NPD2609 Approved
0.5833 Remote Similarity NPD3131 Approved
0.5827 Remote Similarity NPD6309 Approved
0.5827 Remote Similarity NPD6310 Approved
0.5827 Remote Similarity NPD6311 Approved
0.5818 Remote Similarity NPD9512 Approved
0.5814 Remote Similarity NPD3159 Discontinued
0.5814 Remote Similarity NPD2495 Phase 3
0.5806 Remote Similarity NPD6420 Discontinued
0.58 Remote Similarity NPD8414 Discontinued
0.5786 Remote Similarity NPD4686 Approved
0.5786 Remote Similarity NPD4685 Phase 3
0.5786 Remote Similarity NPD4684 Phase 3
0.5781 Remote Similarity NPD7505 Discontinued
0.5769 Remote Similarity NPD2645 Approved
0.5758 Remote Similarity NPD7829 Approved
0.5758 Remote Similarity NPD7830 Approved
0.5758 Remote Similarity NPD616 Clinical (unspecified phase)
0.5738 Remote Similarity NPD4211 Phase 1
0.5727 Remote Similarity NPD9511 Approved
0.5726 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5702 Remote Similarity NPD6698 Approved
0.5702 Remote Similarity NPD46 Approved
0.5676 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5652 Remote Similarity NPD5202 Clinical (unspecified phase)
0.5652 Remote Similarity NPD7983 Approved
0.5652 Remote Similarity NPD6845 Suspended
0.5648 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5641 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5638 Remote Similarity NPD8389 Clinical (unspecified phase)
0.5625 Remote Similarity NPD4249 Approved
0.5619 Remote Similarity NPD1452 Discontinued
0.5606 Remote Similarity NPD6921 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