FAIRMol

MK188

Pose ID 11143 Compound 3911 Pose 300

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 MK188
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.50, H-bond role recall 1.00
Burial
81%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.802 kcal/mol/HA) ✓ Good fit quality (FQ -7.73) ✓ Good H-bonds (5 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (17.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-24.050
kcal/mol
LE
-0.802
kcal/mol/HA
Fit Quality
-7.73
FQ (Leeson)
HAC
30
heavy atoms
MW
459
Da
LogP
4.65
cLogP
Strain ΔE
17.0 kcal/mol
SASA buried
81%
Lipo contact
80% BSA apolar/total
SASA unbound
689 Ų
Apolar buried
445 Ų

Interaction summary

HB 5 HY 24 PI 2 CLASH 2
Final rank1.988Score-24.050
Inter norm-0.769Intra norm-0.033
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 8 clashes; 1 protein clash
Residues
ALA284 ARG228 ARG287 ARG331 GLY196 GLY197 GLY229 GLY286 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER200 SER364 THR374

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: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap10Native recall0.83
Jaccard0.50RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

HB · H-bonds
Mode: permissive. 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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
300 1.988030290479108 -0.769138 -24.0505 4 18 10 0.83 1.00 - no Current
227 3.7064837073857113 -0.959873 -25.1792 12 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 -24.050kcal/mol
Ligand efficiency (LE) -0.8017kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.733
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 459.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.65
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 14.90kcal/mol
Minimised FF energy -2.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 689.0Ų
Total solvent-accessible surface area of free ligand
BSA total 559.8Ų
Buried surface area upon binding
BSA apolar 445.0Ų
Hydrophobic contacts buried
BSA polar 114.8Ų
Polar contacts buried
Fraction buried 81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6538.0Ų
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 2083.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)