jiosephlee/chembl-endpoint-pair-clean-labels huggingface dataset:
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: Activity
- Label type: binary
- Binary semantics: activity
- Assay description: Activation of HDAC2 using Fluor-de-Lys as substrate at 10 uM by spectrofluorometry
- Target name: Histone deacetylase 2
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: O=C(NC(=S)NCCc1ccccc1)c1ccccc1
- Properties:
- ChEMBL ID: CHEMBL1448292
- Molecule type: Small molecule
- Molecular weight: 284.38
- Heavy atoms: 20
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 2
- TPSA: 41.13
- LogP: 2.53
- Rotatable bonds: 4
- Ring count: 2
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.12
- QED: 0.85

## Known Reference Result on This Endpoint
- Molecule A clean result: activity label = 0
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type Activity; comment Not Active

## Query Molecule B
- Canonical SMILES: O=C(NC(=S)NCc1ccccc1)c1ccccc1
- Properties:
- ChEMBL ID: CHEMBL1478462
- Molecule type: Small molecule
- Molecular weight: 270.36
- Heavy atoms: 19
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 2
- TPSA: 41.13
- LogP: 2.49
- Rotatable bonds: 3
- Ring count: 2
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.07
- QED: 0.84

## Molecule Similarity
- Weighted Tanimoto: 0.7

Answer: 0
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Inhibition of BRD4 bromodomain 1/2 (unknown origin) by alphascreen assay
- Assay organism: Homo sapiens
- Target name: Bromodomain-containing protein 4
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: CNc1cc(-c2ccc3cnn(CC4CCCCC4)c3c2)cn(C)c1=O
- Properties:
- ChEMBL ID: CHEMBL4472855
- Molecule type: Unknown
- Molecular weight: 350.47
- Heavy atoms: 26
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 3
- TPSA: 51.85
- LogP: 4.02
- Rotatable bonds: 4
- Ring count: 4
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.43
- QED: 0.77

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 5.74
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 1810; units nM; pChEMBL 5.74

## Query Molecule B
- Canonical SMILES: CCNc1cc(-c2ccc3cnn(Cc4cc(OC)cc(OC)c4)c3c2)cn(C)c1=O
- Properties:
- ChEMBL ID: CHEMBL4460102
- Molecule type: Unknown
- Molecular weight: 418.5
- Heavy atoms: 31
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 5
- TPSA: 70.31
- LogP: 3.9
- Rotatable bonds: 7
- Ring count: 4
- Aromatic rings: 4
- Formal charge: 0
- Fraction Csp3: 0.25
- QED: 0.49

## Molecule Similarity
- Weighted Tanimoto: 0.51

Answer: 5.74
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: Ki
- Label type: continuous
- Binary semantics: pchembl
- Assay description: In vitro binding affinity towards M1 receptor of rat frontal cortex homogenate by using radioligand [3H]QNB
- Assay tissue: Frontal cortex
- Target name: Muscarinic acetylcholine receptor M1
- Target type: SINGLE PROTEIN
- Target organism: Rattus norvegicus

## Reference Molecule A
- Canonical SMILES: Cc1ccc2n1C=C(N1CCN(C)CC1)c1ccccc1S2
- Properties:
- ChEMBL ID: CHEMBL176169
- Molecule type: Small molecule
- Molecular weight: 311.45
- Heavy atoms: 22
- Hydrogen bond donors: 0
- Hydrogen bond acceptors: 3
- TPSA: 11.41
- LogP: 3.46
- Rotatable bonds: 1
- Ring count: 4
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.33
- QED: 0.8

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 5.64
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type Ki; relation =; value 2300; units nM; pChEMBL 5.64

## Query Molecule B
- Canonical SMILES: CN1CCN(C2=Nc3cc(Cl)ccc3Nc3ccccc32)CC1
- Properties:
- ChEMBL ID: CHEMBL42
- Preferred name: CLOZAPINE
- Molecule type: Small molecule
- Max clinical phase: 4
- Molecular weight: 326.83
- Heavy atoms: 23
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 4
- TPSA: 30.87
- LogP: 3.72
- Rotatable bonds: 0
- Ring count: 4
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.28
- QED: 0.8

## Molecule Similarity
- Weighted Tanimoto: 0.28

Answer: 7.27
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: Ki
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Inhibition of human DHFR expressed in Escherichia coli BL21 using DHF as substrate by spectrophotometric analysis
- Assay organism: Homo sapiens
- Target name: Dihydrofolate reductase
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: Br.CC1(C)N=C(N)N=C(N)N1OCCCSc1ccccc1Cl
- Properties:
- ChEMBL ID: CHEMBL4798400
- Molecule type: Unknown
- Molecular weight: 422.78
- Heavy atoms: 23
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 7
- TPSA: 89.23
- LogP: 3.01
- Rotatable bonds: 6
- Ring count: 2
- Aromatic rings: 1
- Formal charge: 0
- Fraction Csp3: 0.43
- QED: 0.54

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 4.68
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type Ki; relation =; value 21100; units nM; pChEMBL 4.68

## Query Molecule B
- Canonical SMILES: Br.CC1(C)N=C(N)N=C(N)N1OCCCNc1ccc(Cl)c(Cl)c1
- Properties:
- ChEMBL ID: CHEMBL4784738
- Molecule type: Unknown
- Molecular weight: 440.17
- Heavy atoms: 24
- Hydrogen bond donors: 3
- Hydrogen bond acceptors: 7
- TPSA: 101.26
- LogP: 2.99
- Rotatable bonds: 6
- Ring count: 2
- Aromatic rings: 1
- Formal charge: 0
- Fraction Csp3: 0.43
- QED: 0.59

## Molecule Similarity
- Weighted Tanimoto: 0.55

Answer: 4.32
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: Activity
- Label type: binary
- Binary semantics: substrate
- Assay description: TP_TRANSPORTER: transepithelial transport (basal to apical) in mdr1b-expressing LLC-PK1 cell
- Assay organism: Mus musculus
- Assay cell type: LLC-PK1
- Target name: ATP-dependent translocase ABCB1
- Target type: SINGLE PROTEIN
- Target organism: Mus musculus

## Reference Molecule A
- Canonical SMILES: CC(C)(C)NC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2CN1C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)[C@H](CC(N)=O)NC(=O)c1ccc2ccccc2n1
- Properties:
- ChEMBL ID: CHEMBL114
- Preferred name: SAQUINAVIR
- Molecule type: Small molecule
- Max clinical phase: 4
- Molecular weight: 670.86
- Heavy atoms: 49
- Hydrogen bond donors: 5
- Hydrogen bond acceptors: 7
- TPSA: 166.75
- LogP: 3.09
- Rotatable bonds: 12
- Ring count: 5
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.5
- QED: 0.2

## Known Reference Result on This Endpoint
- Molecule A clean result: substrate label = 1
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type Activity; comment substrate [+]

## Query Molecule B
- Canonical SMILES: CC(C)c1nc(CN(C)C(=O)N[C@H](C(=O)N[C@@H](Cc2ccccc2)C[C@H](O)[C@H](Cc2ccccc2)NC(=O)OCc2cncs2)C(C)C)cs1
- Properties:
- ChEMBL ID: CHEMBL163
- Preferred name: RITONAVIR
- Molecule type: Small molecule
- Max clinical phase: 4
- Molecular weight: 720.96
- Heavy atoms: 50
- Hydrogen bond donors: 4
- Hydrogen bond acceptors: 9
- TPSA: 145.78
- LogP: 5.91
- Rotatable bonds: 17
- Ring count: 4
- Aromatic rings: 4
- Formal charge: 0
- Fraction Csp3: 0.43
- QED: 0.11

## Molecule Similarity
- Weighted Tanimoto: 0.23

Answer: 1
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Inhibition of bPDGFR in human PAC1 cells
- Assay organism: Homo sapiens
- Assay cell type: PAC1
- Target name: Platelet-derived growth factor receptor beta
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: CCOC(=O)c1c(C)[nH]c(/C=C2\C(=O)Nc3ccccc32)c1C
- Properties:
- ChEMBL ID: CHEMBL86943
- Molecule type: Small molecule
- Molecular weight: 310.35
- Heavy atoms: 23
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 3
- TPSA: 71.19
- LogP: 3.3
- Rotatable bonds: 3
- Ring count: 3
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.22
- QED: 0.67

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 5.4
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 4000; units nM; pChEMBL 5.4

## Query Molecule B
- Canonical SMILES: O=C1Nc2ccccc2/C1=C/c1cc2c([nH]1)CCC(Br)C2
- Properties:
- ChEMBL ID: CHEMBL408565
- Molecule type: Small molecule
- Molecular weight: 343.22
- Heavy atoms: 21
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 1
- TPSA: 44.89
- LogP: 3.76
- Rotatable bonds: 1
- Ring count: 4
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.24
- QED: 0.6

## Molecule Similarity
- Weighted Tanimoto: 0.39

Answer: 6.04
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: Activity
- Label type: binary
- Binary semantics: toxic
- Assay description: Cytotoxicity against human MRC5 at 300 to 400 ug/ml using crystal violet staining
- Assay organism: Homo sapiens
- Assay cell type: MRC5
- Target name: MRC5
- Target type: CELL-LINE
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: CCCOC(=O)[C@]1(O)C=C(OCc2ccc3ccccc3c2)[C@@H](OC(=O)CCC)[C@H](OC(=O)CCC)C1
- Properties:
- ChEMBL ID: CHEMBL1823778
- Molecule type: Small molecule
- Molecular weight: 512.6
- Heavy atoms: 37
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 8
- TPSA: 108.36
- LogP: 4.75
- Rotatable bonds: 12
- Ring count: 3
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.48
- QED: 0.32

## Known Reference Result on This Endpoint
- Molecule A clean result: toxic label = 0
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type Activity; comment Non-toxic

## Query Molecule B
- Canonical SMILES: COC(=O)[C@]1(O)C=C(OCc2cc3ccccc3s2)[C@@H](O)[C@H](O)C1
- Properties:
- ChEMBL ID: CHEMBL1823572
- Molecule type: Small molecule
- Molecular weight: 350.39
- Heavy atoms: 24
- Hydrogen bond donors: 3
- Hydrogen bond acceptors: 7
- TPSA: 96.22
- LogP: 1.33
- Rotatable bonds: 4
- Ring count: 3
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.35
- QED: 0.72

## Molecule Similarity
- Weighted Tanimoto: 0.36

Answer: 0
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: Activity
- Label type: binary
- Binary semantics: activity
- Assay description: Induction of EIF2alpha phosphorylation in human A172 cells at 20 uM measured after 2 hrs by Western blot analysis
- Assay organism: Homo sapiens
- Target name: Eukaryotic translation initiation factor 2 subunit 1
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: N#Cc1cccc(/C=C/C(=O)c2ccc(O)cc2)c1
- Properties:
- ChEMBL ID: CHEMBL4545330
- Molecule type: Unknown
- Molecular weight: 249.27
- Heavy atoms: 19
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 3
- TPSA: 61.09
- LogP: 3.16
- Rotatable bonds: 3
- Ring count: 2
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0
- QED: 0.67

## Known Reference Result on This Endpoint
- Molecule A clean result: activity label = 1
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type Activity; comment Active

## Query Molecule B
- Canonical SMILES: CCCCCN(CCCCC)S(=O)(=O)c1ccc(C(=O)/C=C/c2cccc(O)c2)cc1
- Properties:
- ChEMBL ID: CHEMBL4470548
- Molecule type: Unknown
- Molecular weight: 443.61
- Heavy atoms: 31
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 4
- TPSA: 74.68
- LogP: 5.66
- Rotatable bonds: 13
- Ring count: 2
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.4
- QED: 0.25

## Molecule Similarity
- Weighted Tanimoto: 0.45

Answer: 1
## Endpoint to Predict
- Endpoint scope: target
- Measurement type: ED50
- Label type: continuous
- Binary semantics: pchembl
- Target name: Serine/threonine-protein kinase SIK3
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1nc(-c2cccnc2)nc2c1cnn2C
- Properties:
- ChEMBL ID: CHEMBL3752910
- Molecule type: Small molecule
- Molecular weight: 503.49
- Heavy atoms: 37
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 6
- TPSA: 97.62
- LogP: 5.75
- Rotatable bonds: 5
- Ring count: 5
- Aromatic rings: 5
- Formal charge: 0
- Fraction Csp3: 0.12
- QED: 0.32

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 3.95
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type ED50; relation =; value 111519.14; units nM; pChEMBL 3.95

## Query Molecule B
- Canonical SMILES: Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1nc(-c2cccnc2)nc2nn(C)cc12
- Properties:
- ChEMBL ID: CHEMBL5653589
- Molecular weight: 503.49
- Heavy atoms: 37
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 6
- TPSA: 97.62
- LogP: 5.75
- Rotatable bonds: 5
- Ring count: 5
- Aromatic rings: 5
- Formal charge: 0
- Fraction Csp3: 0.12
- QED: 0.32

## Molecule Similarity
- Weighted Tanimoto: 0.78

Answer: 4.98
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Cytotoxicity against human RD cells assessed as growth inhibition after 48 hrs by MTT method
- Assay organism: Homo sapiens
- Assay cell type: RD
- Target name: RD
- Target type: CELL-LINE
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: COc1cc(C(=O)c2ccn(-c3cccc(N)c3)c2)cc(OC)c1OC
- Properties:
- ChEMBL ID: CHEMBL3318100
- Molecule type: Small molecule
- Molecular weight: 352.39
- Heavy atoms: 26
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 5
- TPSA: 75.71
- LogP: 3.32
- Rotatable bonds: 6
- Ring count: 3
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.15
- QED: 0.54

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 7.02
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 95.3; units nM; pChEMBL 7.02

## Query Molecule B
- Canonical SMILES: CC[C@]1(O)C[C@@H]2CN(CCc3c([nH]c4ccccc34)[C@@](C(=O)OC)(c3cc4c(cc3OC)N(C)[C@H]3[C@@](O)(C(=O)OC)[C@H](OC(C)=O)[C@]5(CC)C=CCN6CC[C@]43[C@@H]65)C2)C1
- Properties:
- ChEMBL ID: CHEMBL159
- Preferred name: VINBLASTINE
- Molecule type: Small molecule
- Max clinical phase: 4
- Molecular weight: 810.99
- Heavy atoms: 59
- Hydrogen bond donors: 3
- Hydrogen bond acceptors: 12
- TPSA: 154.1
- LogP: 3.99
- Rotatable bonds: 7
- Ring count: 9
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.59
- QED: 0.18

## Molecule Similarity
- Weighted Tanimoto: 0.14

Answer: 7.28
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Inhibition of ROCK2 (unknown origin) incubated for 60 mins in presence of ATP by mobility shift assay
- Assay organism: Homo sapiens
- Target name: Rho-associated protein kinase 2
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: CS(=O)(=O)O.CS(=O)(=O)O.NCC(C(=O)Nc1ccc2cnccc2c1)c1ccc(COC(=O)CCCCO[N+](=O)[O-])cc1
- Properties:
- ChEMBL ID: CHEMBL5619370
- Molecular weight: 658.71
- Heavy atoms: 44
- Hydrogen bond donors: 4
- Hydrogen bond acceptors: 12
- TPSA: 255.42
- LogP: 2.35
- Rotatable bonds: 12
- Ring count: 3
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.35
- QED: 0.07

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 8.29
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 5.15; units nM; pChEMBL 8.29

## Query Molecule B
- Canonical SMILES: C[C@H]1CNCCCN1S(=O)(=O)c1cccc2cncc(F)c12
- Properties:
- ChEMBL ID: CHEMBL3426621
- Preferred name: RIPASUDIL
- Molecule type: Small molecule
- Max clinical phase: 3
- Molecular weight: 323.39
- Heavy atoms: 22
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 4
- TPSA: 62.3
- LogP: 1.75
- Rotatable bonds: 2
- Ring count: 3
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.4
- QED: 0.91

## Molecule Similarity
- Weighted Tanimoto: 0.14

Answer: 7.88
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Inhibitory concentration against Pregnane X receptor
- Target name: Nuclear receptor subfamily 1 group I member 2
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: C/C=C1\C(=O)C[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C
- Properties:
- ChEMBL ID: CHEMBL410683
- Preferred name: GUGGULSTERONE
- Molecule type: Small molecule
- Molecular weight: 312.45
- Heavy atoms: 23
- Hydrogen bond donors: 0
- Hydrogen bond acceptors: 2
- TPSA: 34.14
- LogP: 4.64
- Rotatable bonds: 0
- Ring count: 4
- Aromatic rings: 0
- Formal charge: 0
- Fraction Csp3: 0.71
- QED: 0.61

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 8.62
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 2.4; units nM; pChEMBL 8.62

## Query Molecule B
- Canonical SMILES: C/C=C1/C(=O)C[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C
- Properties:
- ChEMBL ID: CHEMBL402063
- Preferred name: E-GUGGULSTERONE
- Molecule type: Small molecule
- Molecular weight: 312.45
- Heavy atoms: 23
- Hydrogen bond donors: 0
- Hydrogen bond acceptors: 2
- TPSA: 34.14
- LogP: 4.64
- Rotatable bonds: 0
- Ring count: 4
- Aromatic rings: 0
- Formal charge: 0
- Fraction Csp3: 0.71
- QED: 0.61

## Molecule Similarity
- Weighted Tanimoto: 1

Answer: 8.62
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Enzymology Assay: 1. Experimental materials and instrumentsPDE9A2 Enzyme (BPS, Cat. No. 60090)384-well plate (Perkin Elmer, Cat. No. 6007279)2. Experimental procedurePreparation of the compounds: the compounds were prepared into 10 mM compound stock solution in DMSO for long-term storage. The obtained compound stock solution was diluted in 100 times with DMSO to obtain 100 μM compound working mother solution, and then the compound working mother solution was diluted in 3 times with DMSO to obtain 8-10 concentration gradients of diluted compound mother liquor (100×).Incubation with the compounds: A very small amount of liquid pipetting system Echo was used to pipette the diluted compound mother liquor into a 384-well plate. 200 nL diluted compound mother liquor and 10 μL PDE9A2 enzyme solution were added to each compound well. After centrifugation at 1000 rpm for 1 min, the mixture was incubated for 15 min at the room temperature. Then the 10 μL substrate mixture was added. After centrifugation at 1000 rpm for 1 min, the mixture was incubated with shocking for 30 min at the room temperature. Finally, a stop solution was added to end the reaction system. The mixture was incubated with shocking for 60 min at the room temperature. In the maximum reading hole (Max), the compound was replaced by solvent. In the minimum reading hole (Min), the compound and enzyme solution were replaced by solvent.
- Assay organism: Homo sapiens
- Target name: High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
- Target type: SINGLE PROTEIN
- Target organism: Homo sapiens

## Reference Molecule A
- Canonical SMILES: N#Cc1c(N2CCC3(CCC3)CC2)c2cc(CO)ncc2[nH]c1=O
- Properties:
- ChEMBL ID: CHEMBL5897878
- Molecular weight: 324.38
- Heavy atoms: 24
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 5
- TPSA: 93.01
- LogP: 2.06
- Rotatable bonds: 2
- Ring count: 4
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.5
- QED: 0.88

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 8.1
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 8; units nM; pChEMBL 8.1; comment 993867

## Query Molecule B
- Canonical SMILES: Cc1cc2c(N3CCC4(CCC4)CC3)c(C#N)c(=O)[nH]c2cn1
- Properties:
- ChEMBL ID: CHEMBL5863416
- Molecular weight: 308.38
- Heavy atoms: 23
- Hydrogen bond donors: 1
- Hydrogen bond acceptors: 4
- TPSA: 72.78
- LogP: 2.87
- Rotatable bonds: 1
- Ring count: 4
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.5
- QED: 0.88

## Molecule Similarity
- Weighted Tanimoto: 0.75

Answer: 7.89
## Endpoint to Predict
- Endpoint scope: assay
- Measurement type: IC50
- Label type: continuous
- Binary semantics: pchembl
- Assay description: Ability to inhibit HIV-1 protease was determined using spectrofluorimetric assay.
- Target name: Human immunodeficiency virus type 1 protease
- Target type: SINGLE PROTEIN
- Target organism: Human immunodeficiency virus 1

## Reference Molecule A
- Canonical SMILES: CCCS(=O)(=O)N(CCC(C)C)C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1ccccc1
- Properties:
- ChEMBL ID: CHEMBL155051
- Molecule type: Small molecule
- Molecular weight: 490.67
- Heavy atoms: 34
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 5
- TPSA: 95.94
- LogP: 3.97
- Rotatable bonds: 14
- Ring count: 2
- Aromatic rings: 2
- Formal charge: 0
- Fraction Csp3: 0.5
- QED: 0.42

## Known Reference Result on This Endpoint
- Molecule A clean result: median pChEMBL = 6.68
- This result is provided as context for predicting Molecule B on the same endpoint.

## Reference Molecule A Other ChEMBL Evidence
- type IC50; relation =; value 210; units nM; pChEMBL 6.68

## Query Molecule B
- Canonical SMILES: CC(C)CCN(C[C@@H](O)[C@H](Cc1ccccc1)NC(=O)OCc1ccccc1)S(=O)(=O)Cc1ccccc1
- Properties:
- ChEMBL ID: CHEMBL155260
- Molecule type: Small molecule
- Molecular weight: 538.71
- Heavy atoms: 38
- Hydrogen bond donors: 2
- Hydrogen bond acceptors: 5
- TPSA: 95.94
- LogP: 4.76
- Rotatable bonds: 14
- Ring count: 3
- Aromatic rings: 3
- Formal charge: 0
- Fraction Csp3: 0.37
- QED: 0.31

## Molecule Similarity
- Weighted Tanimoto: 0.83

Answer: 5