FAIRMol

MK210

Pose ID 11148 Compound 350 Pose 305

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 MK210
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
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
26.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.20, H-bond role recall 0.00
Burial
68%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 69% of hydrophobic surface is solvent-exposed (18/26 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.601 kcal/mol/HA) ✓ Good fit quality (FQ -5.96) ✓ Good H-bonds (3 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (26.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-19.835
kcal/mol
LE
-0.601
kcal/mol/HA
Fit Quality
-5.96
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Final rank
5.3872
rank score
Inter norm
-0.731
normalised
Contacts
18
H-bonds 6
Strain ΔE
26.9 kcal/mol
SASA buried
68%
Lipo contact
82% BSA apolar/total
SASA unbound
777 Ų
Apolar buried
437 Ų

Interaction summary

HBD 1 HBA 2 HY 5 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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

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.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap5Native recall0.42
Jaccard0.20RMSD-
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
322 1.3070478662876737 -0.795495 -22.1443 7 17 0 0.00 0.00 - no Open
239 1.429353830046023 -0.85087 -24.9661 9 18 0 0.00 0.00 - no Open
332 2.109182079251565 -0.787785 -21.1675 4 19 0 0.00 0.00 - no Open
280 2.8384458484406365 -0.771278 -19.4611 11 18 0 0.00 0.00 - no Open
207 2.994404326852969 -0.879267 -22.1427 11 17 0 0.00 0.00 - no Open
228 3.25287543334116 -0.900912 -26.7187 12 18 0 0.00 0.00 - no Open
315 3.7913116092188326 -0.611091 -14.3237 5 14 0 0.00 0.00 - no Open
305 5.387160225431737 -0.730767 -19.8354 6 18 5 0.42 0.00 - 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 -19.835kcal/mol
Ligand efficiency (LE) -0.6011kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.964
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.67
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 52.46kcal/mol
Minimised FF energy 25.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 776.6Ų
Total solvent-accessible surface area of free ligand
BSA total 530.2Ų
Buried surface area upon binding
BSA apolar 437.2Ų
Hydrophobic contacts buried
BSA polar 93.0Ų
Polar contacts buried
Fraction buried 68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6641.0Ų
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 2082.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)