FAIRMol

MK10

Pose ID 11121 Compound 596 Pose 278

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 MK10
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
36.4 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.58, Jaccard 0.28, H-bond role recall 1.00
Burial
80%
Hydrophobic fit
84%
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.784 kcal/mol/HA) ✓ Good fit quality (FQ -7.78) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (36.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-25.882
kcal/mol
LE
-0.784
kcal/mol/HA
Fit Quality
-7.78
FQ (Leeson)
HAC
33
heavy atoms
MW
475
Da
LogP
2.39
cLogP
Strain ΔE
36.4 kcal/mol
SASA buried
80%
Lipo contact
84% BSA apolar/total
SASA unbound
773 Ų
Apolar buried
520 Ų

Interaction summary

HB 6 HY 21 PI 0 CLASH 0
Final rank4.883Score-25.882
Inter norm-0.769Intra norm-0.015
Top1000noExcludedno
Contacts20H-bonds6
Artifact reasongeometry warning; 15 clashes; 3 protein clashes; high strain Δ 36.4
Residues
ALA363 ARG287 ARG331 ARG361 ASP330 CYS375 GLY197 GLY286 GLY376 HIS359 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR360 VAL362

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

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 overlap7Native recall0.58
Jaccard0.28RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
315 3.6546882961068725 -0.7986 -26.4227 2 20 0 0.00 0.00 - no Open
175 4.486397402427168 -0.856708 -23.8486 7 17 0 0.00 0.00 - no Open
278 4.883192618668922 -0.768814 -25.8817 6 20 7 0.58 1.00 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -25.882kcal/mol
Ligand efficiency (LE) -0.7843kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.782
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.39
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.33kcal/mol
Minimised FF energy 61.92kcal/mol

SASA & burial

✓ computed
SASA (unbound) 772.7Ų
Total solvent-accessible surface area of free ligand
BSA total 615.4Ų
Buried surface area upon binding
BSA apolar 520.3Ų
Hydrophobic contacts buried
BSA polar 95.1Ų
Polar contacts buried
Fraction buried 79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6680.6Ų
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 2052.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)