FAIRMol

MK198

Pose ID 11146 Compound 2423 Pose 303

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand MK198
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
37.1 kcal/mol
Protein clashes
2
Internal clashes
6
Native overlap
contact recall 0.75, Jaccard 0.47, H-bond role recall 0.00
Burial
84%
Hydrophobic fit
73%
Reason: 6 internal clashes
2 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.714 kcal/mol/HA) ✓ Good fit quality (FQ -6.58) ✓ Good H-bonds (5 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Very high strain energy (37.1 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (6)
Score
-18.572
kcal/mol
LE
-0.714
kcal/mol/HA
Fit Quality
-6.58
FQ (Leeson)
HAC
26
heavy atoms
MW
400
Da
LogP
0.31
cLogP
Strain ΔE
37.1 kcal/mol
SASA buried
84%
Lipo contact
73% BSA apolar/total
SASA unbound
664 Ų
Apolar buried
403 Ų

Interaction summary

HB 5 HY 24 PI 1 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank0.423Score-18.572
Inter norm-0.857Intra norm0.143
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 6 clashes; 2 protein contact clashes; high strain Δ 37.1
Residues
ALA284 ARG228 ARG287 GLY197 GLY229 GLY286 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER200 SER364 THR374

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.47RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
303 0.42257366008477365 -0.857298 -18.5717 5 16 9 0.75 0.00 - no Current
253 0.6769469302012954 -0.990627 -22.596 4 18 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 -18.572kcal/mol
Ligand efficiency (LE) -0.7143kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.581
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 399.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.31
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 7.61kcal/mol
Minimised FF energy -29.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 663.8Ų
Total solvent-accessible surface area of free ligand
BSA total 554.7Ų
Buried surface area upon binding
BSA apolar 402.7Ų
Hydrophobic contacts buried
BSA polar 152.0Ų
Polar contacts buried
Fraction buried 83.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6507.2Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2053.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)