FAIRMol

MK24

Pose ID 13820 Compound 4172 Pose 262

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T21
T. cruzi R5P T. cruzi
Ligand MK24
PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
45.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.78
Burial
70%
Hydrophobic fit
77%
Reason: strain 45.3 kcal/mol
strain ΔE 45.3 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 62% of hydrophobic surface is solvent-exposed (16/26 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.579 kcal/mol/HA) ✓ Good fit quality (FQ -5.83) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Extreme strain energy (45.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-20.247
kcal/mol
LE
-0.579
kcal/mol/HA
Fit Quality
-5.83
FQ (Leeson)
HAC
35
heavy atoms
MW
503
Da
LogP
2.03
cLogP
Final rank
4.3576
rank score
Inter norm
-0.720
normalised
Contacts
18
H-bonds 13
Strain ΔE
45.3 kcal/mol
SASA buried
70%
Lipo contact
77% BSA apolar/total
SASA unbound
758 Ų
Apolar buried
405 Ų

Interaction summary

HBA 10 HY 3 PI 3 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap13Native recall0.93
Jaccard0.68RMSD-
HB strict9Strict recall0.75
HB same residue+role7HB role recall0.78
HB same residue7HB residue recall0.88

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
280 3.072939621275057 -0.652326 -26.0627 9 14 0 0.00 0.00 - no Open
262 4.357606610843862 -0.719793 -20.2471 13 18 13 0.93 0.78 - no Current
352 4.377816770020476 -0.688479 -23.3913 4 15 0 0.00 0.00 - no Open
299 4.8568129299279565 -0.590291 -13.2375 6 10 0 0.00 0.00 - no Open
221 5.152576031245613 -0.894038 -31.6518 8 16 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -20.247kcal/mol
Ligand efficiency (LE) -0.5785kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.835
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 502.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 102.73kcal/mol
Minimised FF energy 57.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 758.5Ų
Total solvent-accessible surface area of free ligand
BSA total 528.3Ų
Buried surface area upon binding
BSA apolar 404.8Ų
Hydrophobic contacts buried
BSA polar 123.5Ų
Polar contacts buried
Fraction buried 69.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2358.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 754.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)