Structure

Physi-Chem Properties

Molecular Weight:  314.14
Volume:  303.169
LogP:  1.115
LogD:  0.717
LogS:  -0.497
# Rotatable Bonds:  10
TPSA:  83.91
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.244
Synthetic Accessibility Score:  3.137
Fsp3:  0.615
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:  -5.506
MDCK Permeability:  2.4989003577502444e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.042
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.72
Plasma Protein Binding (PPB):  18.804046630859375%
Volume Distribution (VD):  1.871
Pgp-substrate:  84.66726684570312%

ADMET: Metabolism

CYP1A2-inhibitor:  0.033
CYP1A2-substrate:  0.642
CYP2C19-inhibitor:  0.059
CYP2C19-substrate:  0.884
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.209
CYP2D6-inhibitor:  0.318
CYP2D6-substrate:  0.922
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.204

ADMET: Excretion

Clearance (CL):  12.245
Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.752
Drug-inuced Liver Injury (DILI):  0.57
AMES Toxicity:  0.597
Rat Oral Acute Toxicity:  0.749
Maximum Recommended Daily Dose:  0.41
Skin Sensitization:  0.657
Carcinogencity:  0.854
Eye Corrosion:  0.003
Eye Irritation:  0.014
Respiratory Toxicity:  0.914

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

  Natural Product: NPC320751

Natural Product ID:  NPC320751
Common Name*:   Ranitidine
IUPAC Name:   (E)-1-N'-[2-[[5-[(dimethylamino)methyl]furan-2-yl]methylsulfanyl]ethyl]-1-N-methyl-2-nitroethene-1,1-diamine
Synonyms:  
Standard InCHIKey:  VMXUWOKSQNHOCA-UKTHLTGXSA-N
Standard InCHI:  InChI=1S/C13H22N4O3S/c1-14-13(9-17(18)19)15-6-7-21-10-12-5-4-11(20-12)8-16(2)3/h4-5,9,14-15H,6-8,10H2,1-3H3/b13-9+
SMILES:  CNC(=C[N+](=O)[O-])NCCSCC1=CC=C(O1)CN(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL512
PubChem CID:   3001055
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0002449] Amines
          • [CHEMONTID:0003899] Aralkylamines

*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

☑ 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
NPT492 Cell Line Caco-2 Homo sapiens Ratio = 3.24 n.a. PMID[526829]
NPT109 Individual Protein Cytochrome P450 3A4 Homo sapiens FC = 3.3 n.a. PMID[526839]
NPT110 Individual Protein Cytochrome P450 2D6 Homo sapiens FC = 3.8 n.a. PMID[526839]
NPT212 Individual Protein Cytochrome P450 2C9 Homo sapiens FC = 1.0 n.a. PMID[526839]
NPT27 Others Unspecified Papp = 0.084 10'-6 cm/s PMID[526816]
NPT27 Others Unspecified Papp = 1.9 10'-6 cm/s PMID[526816]
NPT27 Others Unspecified Ratio = 22.6 n.a. PMID[526816]
NPT27 Others Unspecified Drug recovery = 85.0 % PMID[526817]
NPT27 Others Unspecified permeability = 3.7 10'-6 cm/s PMID[526817]
NPT27 Others Unspecified Papp = 0.2 10'-6 cm/s PMID[526818]
NPT27 Others Unspecified Papp = 1.7 10'-6 cm/s PMID[526818]
NPT27 Others Unspecified Ratio = 8.5 n.a. PMID[526818]
NPT27 Others Unspecified Peff = 0.1 10'-6 cm/s PMID[526819]
NPT27 Others Unspecified Peff = 0.2 10'-6 cm/s PMID[526819]
NPT713 Individual Protein Bile salt export pump Homo sapiens IC50 > 135000.0 nM PMID[526820]
NPT27 Others Unspecified Papp = 0.235 10'-6 cm/s PMID[526821]
NPT27 Others Unspecified Papp = 2.31 10'-6 cm/s PMID[526821]
NPT27 Others Unspecified Ratio = 9.8 n.a. PMID[526821]
NPT713 Individual Protein Bile salt export pump Homo sapiens IC50 > 1000000.0 nM PMID[526822]
NPT27 Others Unspecified Ratio = 8.1 n.a. PMID[526823]
NPT27 Others Unspecified Papp = 1.3 ucm/s PMID[526823]
NPT27 Others Unspecified Papp = 0.2 ucm/s PMID[526823]
NPT605 Organism Homo sapiens Homo sapiens DILI_severity_class = 5.0 n.a. PMID[526824]
NPT27 Others Unspecified Papp = 0.45 ucm/s PMID[526825]
NPT27 Others Unspecified Papp = 1.2 ucm/s PMID[526825]
NPT27 Others Unspecified Ratio = 2.7 n.a. PMID[526825]
NPT27 Others Unspecified Ratio = 8.0 n.a. PMID[526826]
NPT27 Others Unspecified Papp = 1.2 10'-6 cm/s PMID[526826]
NPT27 Others Unspecified Papp = 0.15 10'-6 cm/s PMID[526826]
NPT27 Others Unspecified Papp = 0.33 10'-6 cm/s PMID[526827]
NPT27 Others Unspecified Papp = 2.4 10'-6 cm/s PMID[526827]
NPT27 Others Unspecified Ratio = 7.3 n.a. PMID[526827]
NPT27 Others Unspecified Papp = 0.2 10'-6 cm/s PMID[526828]
NPT27 Others Unspecified Papp = 1.7 10'-6 cm/s PMID[526828]
NPT27 Others Unspecified Ratio = 8.5 n.a. PMID[526828]
NPT27 Others Unspecified Papp = 0.87 ucm/s PMID[526829]
NPT27 Others Unspecified Papp = 2.83 ucm/s PMID[526829]
NPT27 Others Unspecified Papp = 0.27 ucm/s PMID[526830]
NPT27 Others Unspecified Papp = 1.71 ucm/s PMID[526830]
NPT27 Others Unspecified Ratio = 6.3 n.a. PMID[526830]
NPT27 Others Unspecified Papp = 0.237 10'-6 cm/s PMID[526831]
NPT27 Others Unspecified Papp = 1.14 10'-6 cm/s PMID[526831]
NPT27 Others Unspecified Ratio = 5.0 n.a. PMID[526831]
NPT35 Others n.a. permeability = 0.5 ucm/s PMID[526832]
NPT35 Others n.a. permeability = 0.1 ucm/s PMID[526832]
NPT27 Others Unspecified Papp = 0.3 10'-6 cm/s PMID[526833]
NPT27 Others Unspecified Papp = 2.0 10'-6 cm/s PMID[526833]
NPT35 Others n.a. Peff = 0.04 10'-6 cm/s PMID[526834]
NPT35 Others n.a. Peff = 0.5 10'-6 cm/s PMID[526835]
NPT35 Others n.a. Peff = 0.62 10'-6 cm/s PMID[526835]
NPT35 Others n.a. Fa = 87.3 % PMID[526835]
NPT35 Others n.a. log Pe = -8.02 n.a. PMID[526836]
NPT21075 SINGLE PROTEIN Cholesterol 24-hydroxylase Homo sapiens Activity = 9.0 % PMID[526837]
NPT35 Others n.a. Peff = 0.0 10'-6 cm/s PMID[526838]
NPT35 Others n.a. permeability = 0.0 % PMID[526838]
NPT27 Others Unspecified Papp = 0.5 10^-6 cm/s PMID[526840]
NPT27 Others Unspecified Papp = 1.3 10^-6 cm/s PMID[526840]
NPT27 Others Unspecified Peff = 0.35 10^-6 cm/s PMID[526841]
NPT27 Others Unspecified Drugabsorption = 13.48 % PMID[526842]
NPT27 Others Unspecified permeability = 0.38 10^-6 cm/s PMID[526842]
NPT27 Others Unspecified permeability = 0.5 10^-6 cm/s PMID[526842]

☑ 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 NPC320751 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
0.6871 Remote Similarity NPC325857
0.6127 Remote Similarity NPC471646
0.6127 Remote Similarity NPC471647
0.6084 Remote Similarity NPC233791
0.6073 Remote Similarity NPC235194
0.5944 Remote Similarity NPC471649
0.5941 Remote Similarity NPC307682
0.5839 Remote Similarity NPC156768
0.5806 Remote Similarity NPC471652
0.5798 Remote Similarity NPC471648
0.5782 Remote Similarity NPC146316
0.5765 Remote Similarity NPC266425
0.5764 Remote Similarity NPC268170
0.5763 Remote Similarity NPC189908
0.5752 Remote Similarity NPC298087
0.5752 Remote Similarity NPC42471
0.5751 Remote Similarity NPC288305
0.5737 Remote Similarity NPC473245
0.5737 Remote Similarity NPC176304
0.5737 Remote Similarity NPC70840
0.5714 Remote Similarity NPC26589
0.5714 Remote Similarity NPC87391
0.5714 Remote Similarity NPC473444
0.5698 Remote Similarity NPC223873
0.5692 Remote Similarity NPC76433
0.5692 Remote Similarity NPC186957
0.5692 Remote Similarity NPC289167
0.5691 Remote Similarity NPC471651
0.567 Remote Similarity NPC197335
0.5648 Remote Similarity NPC469964
0.5648 Remote Similarity NPC476236
0.5648 Remote Similarity NPC472474
0.5644 Remote Similarity NPC108847
0.5641 Remote Similarity NPC314659
0.5635 Remote Similarity NPC297647
0.5634 Remote Similarity NPC50511
0.5632 Remote Similarity NPC216149
0.5632 Remote Similarity NPC208170
0.5625 Remote Similarity NPC11821
0.5616 Remote Similarity NPC163867
0.5614 Remote Similarity NPC208022
0.5613 Remote Similarity NPC219969
0.5606 Remote Similarity NPC329731
0.5604 Remote Similarity NPC13397
0.56 Remote Similarity NPC313918

  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 NPC320751 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
1.0 High Similarity NPD1142 Approved
1.0 High Similarity NPD1141 Approved
1.0 High Similarity NPD1140 Approved
1.0 High Similarity NPD1143 Approved
0.7799 Intermediate Similarity NPD3613 Discontinued
0.7267 Intermediate Similarity NPD4799 Discontinued
0.7174 Intermediate Similarity NPD3659 Discontinued
0.7011 Intermediate Similarity NPD6103 Clinical (unspecified phase)
0.6648 Remote Similarity NPD246 Approved
0.663 Remote Similarity NPD1639 Discontinued
0.6629 Remote Similarity NPD504 Phase 2
0.6497 Remote Similarity NPD419 Approved
0.6448 Remote Similarity NPD918 Approved
0.6404 Remote Similarity NPD9473 Approved
0.6402 Remote Similarity NPD2542 Clinical (unspecified phase)
0.6389 Remote Similarity NPD5262 Discontinued
0.6364 Remote Similarity NPD4078 Clinical (unspecified phase)
0.6333 Remote Similarity NPD9474 Approved
0.6327 Remote Similarity NPD4496 Clinical (unspecified phase)
0.6229 Remote Similarity NPD9085 Approved
0.6209 Remote Similarity NPD9069 Phase 1
0.6201 Remote Similarity NPD9479 Approved
0.6201 Remote Similarity NPD9478 Approved
0.6198 Remote Similarity NPD1986 Approved
0.6186 Remote Similarity NPD3958 Approved
0.6178 Remote Similarity NPD1987 Approved
0.6178 Remote Similarity NPD1985 Approved
0.6165 Remote Similarity NPD2547 Discontinued
0.6158 Remote Similarity NPD3874 Discontinued
0.6111 Remote Similarity NPD3291 Approved
0.6096 Remote Similarity NPD3050 Clinical (unspecified phase)
0.6044 Remote Similarity NPD1307 Phase 2
0.6044 Remote Similarity NPD1309 Phase 2
0.604 Remote Similarity NPD4467 Phase 2
0.604 Remote Similarity NPD4465 Phase 2
0.6011 Remote Similarity NPD4503 Phase 2
0.5989 Remote Similarity NPD3873 Phase 3
0.5989 Remote Similarity NPD3869 Phase 3
0.5946 Remote Similarity NPD2681 Approved
0.5946 Remote Similarity NPD2680 Approved
0.5941 Remote Similarity NPD743 Approved
0.5916 Remote Similarity NPD5192 Clinical (unspecified phase)
0.59 Remote Similarity NPD1198 Approved
0.5892 Remote Similarity NPD3861 Approved
0.5892 Remote Similarity NPD3862 Approved
0.5879 Remote Similarity NPD3964 Approved
0.5865 Remote Similarity NPD7272 Discontinued
0.5859 Remote Similarity NPD1059 Phase 2
0.5858 Remote Similarity NPD4101 Phase 1
0.5856 Remote Similarity NPD4205 Phase 3
0.5852 Remote Similarity NPD160 Clinical (unspecified phase)
0.5851 Remote Similarity NPD2248 Approved
0.5851 Remote Similarity NPD2246 Approved
0.5846 Remote Similarity NPD4084 Clinical (unspecified phase)
0.5843 Remote Similarity NPD2186 Approved
0.5842 Remote Similarity NPD5228 Phase 3
0.5842 Remote Similarity NPD1199 Approved
0.5842 Remote Similarity NPD1200 Approved
0.5833 Remote Similarity NPD5152 Clinical (unspecified phase)
0.5829 Remote Similarity NPD1562 Clinical (unspecified phase)
0.5799 Remote Similarity NPD2245 Discovery
0.5785 Remote Similarity NPD946 Discontinued
0.5782 Remote Similarity NPD4679 Discontinued
0.5775 Remote Similarity NPD2249 Approved
0.5775 Remote Similarity NPD2247 Approved
0.5765 Remote Similarity NPD1393 Approved
0.5755 Remote Similarity NPD1960 Phase 2
0.5746 Remote Similarity NPD2512 Phase 3
0.5745 Remote Similarity NPD5668 Clinical (unspecified phase)
0.5735 Remote Similarity NPD6321 Discontinued
0.573 Remote Similarity NPD1801 Approved
0.573 Remote Similarity NPD1802 Approved
0.5723 Remote Similarity NPD2164 Clinical (unspecified phase)
0.57 Remote Similarity NPD4466 Phase 1
0.57 Remote Similarity NPD4130 Phase 3
0.5693 Remote Similarity NPD5564 Approved
0.5691 Remote Similarity NPD3511 Discontinued
0.5687 Remote Similarity NPD5480 Clinical (unspecified phase)
0.5684 Remote Similarity NPD4575 Clinical (unspecified phase)
0.5684 Remote Similarity NPD1194 Discontinued
0.5684 Remote Similarity NPD3451 Clinical (unspecified phase)
0.5682 Remote Similarity NPD965 Approved
0.5679 Remote Similarity NPD2595 Approved
0.5679 Remote Similarity NPD2594 Approved
0.5676 Remote Similarity NPD5616 Clinical (unspecified phase)
0.5674 Remote Similarity NPD1084 Clinical (unspecified phase)
0.5673 Remote Similarity NPD3142 Approved
0.5673 Remote Similarity NPD3140 Approved
0.5667 Remote Similarity NPD6890 Discontinued
0.5663 Remote Similarity NPD927 Approved
0.5661 Remote Similarity NPD5186 Approved
0.5661 Remote Similarity NPD5183 Approved
0.5659 Remote Similarity NPD2052 Approved
0.5657 Remote Similarity NPD1276 Clinical (unspecified phase)
0.5648 Remote Similarity NPD692 Approved
0.5641 Remote Similarity NPD7190 Clinical (unspecified phase)
0.5635 Remote Similarity NPD1670 Discontinued
0.5634 Remote Similarity NPD429 Approved
0.5632 Remote Similarity NPD3693 Clinical (unspecified phase)
0.5631 Remote Similarity NPD7626 Approved
0.5631 Remote Similarity NPD7627 Approved
0.5631 Remote Similarity NPD3442 Approved
0.5631 Remote Similarity NPD6863 Phase 2
0.5631 Remote Similarity NPD3441 Approved
0.5628 Remote Similarity NPD4258 Approved
0.5628 Remote Similarity NPD2053 Approved
0.5628 Remote Similarity NPD22 Approved
0.5628 Remote Similarity NPD4259 Approved
0.5625 Remote Similarity NPD5719 Approved
0.5622 Remote Similarity NPD5041 Clinical (unspecified phase)
0.5613 Remote Similarity NPD5374 Approved
0.5613 Remote Similarity NPD5373 Approved
0.5611 Remote Similarity NPD4662 Approved
0.5611 Remote Similarity NPD4661 Approved
0.5607 Remote Similarity NPD442 Discontinued
0.5606 Remote Similarity NPD2942 Phase 2
0.5604 Remote Similarity NPD3802 Phase 3
0.56 Remote Similarity NPD1422 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