Structure

Physi-Chem Properties

Molecular Weight:  202.08
Volume:  182.502
LogP:  0.214
LogD:  0.029
LogS:  -1.325
# Rotatable Bonds:  0
TPSA:  79.15
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.444
Synthetic Accessibility Score:  4.905
Fsp3:  1.0
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:  -5.305
MDCK Permeability:  0.0001155267673311755
Pgp-inhibitor:  0.001
Pgp-substrate:  0.889
Human Intestinal Absorption (HIA):  0.434
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.402

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.56
Plasma Protein Binding (PPB):  17.043212890625%
Volume Distribution (VD):  0.71
Pgp-substrate:  76.36945343017578%

ADMET: Metabolism

CYP1A2-inhibitor:  0.016
CYP1A2-substrate:  0.633
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.628
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.063
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.076

ADMET: Excretion

Clearance (CL):  2.072
Half-life (T1/2):  0.682

ADMET: Toxicity

hERG Blockers:  0.044
Human Hepatotoxicity (H-HT):  0.199
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.509
Rat Oral Acute Toxicity:  0.104
Maximum Recommended Daily Dose:  0.009
Skin Sensitization:  0.419
Carcinogencity:  0.589
Eye Corrosion:  0.143
Eye Irritation:  0.764
Respiratory Toxicity:  0.649

Download Data

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

  Natural Product: NPC248427

Natural Product ID:  NPC248427
Common Name*:   Rehmaglutin A
IUPAC Name:   n.a.
Synonyms:   Rehmaglutin A
Standard InCHIKey:  QMQZZRSFTSGWJA-FJYMVOSHSA-N
Standard InCHI:  InChI=1S/C9H14O5/c10-6-4-1-2-13-8-5(4)9(12,3-14-8)7(6)11/h4-8,10-12H,1-3H2/t4-,5-,6+,7-,8-,9-/m1/s1
SMILES:  O[C@H]1[C@@H]2CCO[C@H]3[C@@H]2[C@]([C@@H]1O)(O)CO3
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2332356
PubChem CID:   5320903
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0001565] Iridoids 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
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota Roots n.a. n.a. PMID[22916954]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18120 Radix rehmanniae Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8101 Rehmannia glutinosa Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8101 Rehmannia glutinosa Species Orobanchaceae 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
NPT918 Individual Protein Heat shock protein HSP 90-alpha Homo sapiens Kd = 2388.0 nM PMID[539130]

☑ 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 NPC248427 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
0.8873 High Similarity NPC470659
0.8873 High Similarity NPC470660
0.8767 High Similarity NPC279575
0.8667 High Similarity NPC170595
0.7922 Intermediate Similarity NPC188793
0.7683 Intermediate Similarity NPC474156
0.7619 Intermediate Similarity NPC31349
0.7619 Intermediate Similarity NPC472396
0.7531 Intermediate Similarity NPC216941
0.75 Intermediate Similarity NPC470657
0.7471 Intermediate Similarity NPC59006
0.7439 Intermediate Similarity NPC475849
0.7416 Intermediate Similarity NPC473065
0.7416 Intermediate Similarity NPC473067
0.7416 Intermediate Similarity NPC474399
0.7416 Intermediate Similarity NPC473064
0.7412 Intermediate Similarity NPC258501
0.7386 Intermediate Similarity NPC167644
0.7386 Intermediate Similarity NPC311246
0.7356 Intermediate Similarity NPC473542
0.7349 Intermediate Similarity NPC474266
0.7326 Intermediate Similarity NPC148534
0.7326 Intermediate Similarity NPC470009
0.7308 Intermediate Similarity NPC166250
0.7308 Intermediate Similarity NPC138273
0.7303 Intermediate Similarity NPC3538
0.7303 Intermediate Similarity NPC113500
0.7303 Intermediate Similarity NPC175
0.7303 Intermediate Similarity NPC30687
0.7303 Intermediate Similarity NPC477224
0.7303 Intermediate Similarity NPC45959
0.7303 Intermediate Similarity NPC252253
0.7294 Intermediate Similarity NPC149018
0.7294 Intermediate Similarity NPC171484
0.7273 Intermediate Similarity NPC36372
0.7273 Intermediate Similarity NPC5632
0.7273 Intermediate Similarity NPC149966
0.7273 Intermediate Similarity NPC235051
0.7262 Intermediate Similarity NPC98276
0.7262 Intermediate Similarity NPC259296
0.7253 Intermediate Similarity NPC274200
0.7253 Intermediate Similarity NPC233649
0.7253 Intermediate Similarity NPC470028
0.725 Intermediate Similarity NPC214030
0.725 Intermediate Similarity NPC70996
0.725 Intermediate Similarity NPC83108
0.7241 Intermediate Similarity NPC228059
0.7241 Intermediate Similarity NPC102725
0.7241 Intermediate Similarity NPC22918
0.7241 Intermediate Similarity NPC20822
0.7241 Intermediate Similarity NPC82955
0.7209 Intermediate Similarity NPC210658
0.7209 Intermediate Similarity NPC161928
0.72 Intermediate Similarity NPC477758
0.72 Intermediate Similarity NPC477761
0.72 Intermediate Similarity NPC477760
0.72 Intermediate Similarity NPC477754
0.72 Intermediate Similarity NPC477759
0.7191 Intermediate Similarity NPC144790
0.7191 Intermediate Similarity NPC149400
0.7191 Intermediate Similarity NPC249204
0.7191 Intermediate Similarity NPC234352
0.7191 Intermediate Similarity NPC88962
0.7191 Intermediate Similarity NPC177834
0.7191 Intermediate Similarity NPC297348
0.7191 Intermediate Similarity NPC477451
0.7191 Intermediate Similarity NPC141769
0.7191 Intermediate Similarity NPC277774
0.7191 Intermediate Similarity NPC477547
0.7191 Intermediate Similarity NPC325828
0.7191 Intermediate Similarity NPC250393
0.7191 Intermediate Similarity NPC48339
0.7176 Intermediate Similarity NPC290612
0.7159 Intermediate Similarity NPC279329
0.7159 Intermediate Similarity NPC223143
0.7143 Intermediate Similarity NPC304011
0.7143 Intermediate Similarity NPC219040
0.7143 Intermediate Similarity NPC471879
0.7143 Intermediate Similarity NPC476510
0.7143 Intermediate Similarity NPC142264
0.7143 Intermediate Similarity NPC139271
0.7126 Intermediate Similarity NPC281004
0.7126 Intermediate Similarity NPC128475
0.7111 Intermediate Similarity NPC179859
0.7111 Intermediate Similarity NPC312678
0.7111 Intermediate Similarity NPC264101
0.7111 Intermediate Similarity NPC291547
0.7111 Intermediate Similarity NPC291203
0.7111 Intermediate Similarity NPC294686
0.7111 Intermediate Similarity NPC24960
0.7111 Intermediate Similarity NPC309866
0.7111 Intermediate Similarity NPC475436
0.7111 Intermediate Similarity NPC217205
0.7111 Intermediate Similarity NPC473774
0.7111 Intermediate Similarity NPC174024
0.7111 Intermediate Similarity NPC222731
0.7111 Intermediate Similarity NPC253268
0.7111 Intermediate Similarity NPC471464
0.7111 Intermediate Similarity NPC473851
0.7111 Intermediate Similarity NPC131693
0.7089 Intermediate Similarity NPC308489
0.7083 Intermediate Similarity NPC472026
0.7079 Intermediate Similarity NPC210759
0.7079 Intermediate Similarity NPC229801
0.7079 Intermediate Similarity NPC307167
0.7079 Intermediate Similarity NPC276298
0.7079 Intermediate Similarity NPC293609
0.7067 Intermediate Similarity NPC477764
0.7067 Intermediate Similarity NPC477756
0.7067 Intermediate Similarity NPC477752
0.7067 Intermediate Similarity NPC477751
0.7065 Intermediate Similarity NPC477223
0.7065 Intermediate Similarity NPC477222
0.7065 Intermediate Similarity NPC470684
0.7065 Intermediate Similarity NPC470683
0.7059 Intermediate Similarity NPC227260
0.7045 Intermediate Similarity NPC473472
0.7033 Intermediate Similarity NPC92196
0.7033 Intermediate Similarity NPC107188
0.7033 Intermediate Similarity NPC473610
0.7033 Intermediate Similarity NPC211354
0.7033 Intermediate Similarity NPC475351
0.7033 Intermediate Similarity NPC19400
0.7033 Intermediate Similarity NPC473727
0.7033 Intermediate Similarity NPC107962
0.7033 Intermediate Similarity NPC206003
0.7033 Intermediate Similarity NPC6295
0.7027 Intermediate Similarity NPC476702
0.7024 Intermediate Similarity NPC470611
0.7011 Intermediate Similarity NPC43912
0.7011 Intermediate Similarity NPC140446
0.6989 Remote Similarity NPC473638
0.6989 Remote Similarity NPC291548
0.6977 Remote Similarity NPC232044
0.6977 Remote Similarity NPC273290
0.6966 Remote Similarity NPC65550
0.6957 Remote Similarity NPC128572
0.6957 Remote Similarity NPC98018
0.6957 Remote Similarity NPC121453
0.6957 Remote Similarity NPC470863
0.6957 Remote Similarity NPC84111
0.6957 Remote Similarity NPC473601
0.6957 Remote Similarity NPC103616
0.6957 Remote Similarity NPC475625
0.6957 Remote Similarity NPC470865
0.6957 Remote Similarity NPC30856
0.6957 Remote Similarity NPC470864
0.6957 Remote Similarity NPC156377
0.6957 Remote Similarity NPC287483
0.6957 Remote Similarity NPC470866
0.6957 Remote Similarity NPC195297
0.6957 Remote Similarity NPC475643
0.6957 Remote Similarity NPC97700
0.6957 Remote Similarity NPC132080
0.6957 Remote Similarity NPC473287
0.6957 Remote Similarity NPC116756
0.6957 Remote Similarity NPC284104
0.6957 Remote Similarity NPC232037
0.6957 Remote Similarity NPC184617
0.6957 Remote Similarity NPC160426
0.6951 Remote Similarity NPC177343
0.6951 Remote Similarity NPC272841
0.6947 Remote Similarity NPC470029
0.6947 Remote Similarity NPC134967
0.6947 Remote Similarity NPC114700
0.6947 Remote Similarity NPC310138
0.6941 Remote Similarity NPC69953
0.6933 Remote Similarity NPC165069
0.6923 Remote Similarity NPC473503
0.6923 Remote Similarity NPC475325
0.6923 Remote Similarity NPC305418
0.6915 Remote Similarity NPC470030
0.6901 Remote Similarity NPC119425
0.6901 Remote Similarity NPC322148
0.6897 Remote Similarity NPC107603
0.6897 Remote Similarity NPC268633
0.6897 Remote Similarity NPC471240
0.6889 Remote Similarity NPC274274
0.6889 Remote Similarity NPC473150
0.6889 Remote Similarity NPC473637
0.6889 Remote Similarity NPC294643
0.6889 Remote Similarity NPC473830
0.6889 Remote Similarity NPC476668
0.6889 Remote Similarity NPC204881
0.6882 Remote Similarity NPC307534
0.6882 Remote Similarity NPC470861
0.6882 Remote Similarity NPC476112
0.6882 Remote Similarity NPC470862
0.6882 Remote Similarity NPC51520
0.6882 Remote Similarity NPC83137
0.6882 Remote Similarity NPC303069
0.6882 Remote Similarity NPC261372
0.6882 Remote Similarity NPC475207
0.6882 Remote Similarity NPC263674
0.6882 Remote Similarity NPC232611
0.6882 Remote Similarity NPC115165
0.6882 Remote Similarity NPC58267
0.6875 Remote Similarity NPC470630
0.6866 Remote Similarity NPC323574
0.6854 Remote Similarity NPC50464

  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 NPC248427 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
0.7191 Intermediate Similarity NPD8171 Discontinued
0.6812 Remote Similarity NPD894 Approved
0.6812 Remote Similarity NPD895 Approved
0.6812 Remote Similarity NPD887 Approved
0.6812 Remote Similarity NPD889 Approved
0.6786 Remote Similarity NPD6928 Phase 2
0.6761 Remote Similarity NPD2267 Suspended
0.6667 Remote Similarity NPD1811 Approved
0.6667 Remote Similarity NPD1810 Approved
0.6633 Remote Similarity NPD4056 Clinical (unspecified phase)
0.6633 Remote Similarity NPD4057 Clinical (unspecified phase)
0.6522 Remote Similarity NPD905 Approved
0.6522 Remote Similarity NPD904 Phase 3
0.6465 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6364 Remote Similarity NPD371 Approved
0.6338 Remote Similarity NPD891 Phase 3
0.6338 Remote Similarity NPD888 Phase 3
0.6338 Remote Similarity NPD893 Approved
0.6338 Remote Similarity NPD892 Phase 3
0.6338 Remote Similarity NPD890 Clinical (unspecified phase)
0.6296 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6269 Remote Similarity NPD8998 Phase 2
0.6269 Remote Similarity NPD9000 Phase 3
0.6269 Remote Similarity NPD8993 Phase 1
0.6269 Remote Similarity NPD8999 Phase 3
0.6269 Remote Similarity NPD8997 Approved
0.6197 Remote Similarity NPD2269 Approved
0.6098 Remote Similarity NPD2687 Approved
0.6098 Remote Similarity NPD2686 Approved
0.6098 Remote Similarity NPD2254 Approved
0.6087 Remote Similarity NPD8965 Approved
0.6087 Remote Similarity NPD8966 Approved
0.6026 Remote Similarity NPD847 Phase 1
0.597 Remote Similarity NPD9006 Approved
0.5865 Remote Similarity NPD6412 Phase 2
0.5824 Remote Similarity NPD3669 Approved
0.5824 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5821 Remote Similarity NPD8788 Approved
0.5816 Remote Similarity NPD7991 Discontinued
0.5795 Remote Similarity NPD4238 Approved
0.5795 Remote Similarity NPD4802 Phase 2
0.5769 Remote Similarity NPD6123 Approved
0.5766 Remote Similarity NPD7328 Approved
0.5766 Remote Similarity NPD7327 Approved
0.5752 Remote Similarity NPD8033 Approved
0.575 Remote Similarity NPD1457 Discontinued
0.5714 Remote Similarity NPD7516 Approved
0.5686 Remote Similarity NPD1700 Approved
0.5676 Remote Similarity NPD9036 Phase 3
0.5676 Remote Similarity NPD9035 Clinical (unspecified phase)
0.5664 Remote Similarity NPD8377 Approved
0.5664 Remote Similarity NPD8294 Approved
0.5614 Remote Similarity NPD8380 Approved
0.5614 Remote Similarity NPD8296 Approved
0.5614 Remote Similarity NPD8379 Approved
0.5614 Remote Similarity NPD8378 Approved
0.5614 Remote Similarity NPD8335 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