FAIRMol

MK131

Pose ID 13185 Compound 4954 Pose 306

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand MK131
PDB9IFH↗

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
72.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.78, H-bond role recall 0.00
Burial
50%
Hydrophobic fit
66%
Reason: strain 72.3 kcal/mol
strain ΔE 72.3 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.784 kcal/mol/HA) ✓ Good fit quality (FQ -7.40) ✓ Strong H-bond network (10 bonds) ✓ Good burial (50% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (72.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-21.953
kcal/mol
LE
-0.784
kcal/mol/HA
Fit Quality
-7.40
FQ (Leeson)
HAC
28
heavy atoms
MW
395
Da
LogP
0.29
cLogP
Strain ΔE
72.3 kcal/mol
SASA buried
50%
Lipo contact
66% BSA apolar/total
SASA unbound
633 Ų
Apolar buried
208 Ų

Interaction summary

HB 10 HY 9 PI 1 CLASH 1

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
Final rank3.650Score-21.953
Inter norm-0.682Intra norm-0.102
Top1000noExcludedno
Contacts8H-bonds10
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; high strain Δ 72.3
Residues
ASN402 GLU467 LEU399 LYS410 PHE396 PRO398 SER394 THR397

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap7Native recall0.88
Jaccard0.78RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
274 3.330596933897339 -0.751008 -28.3633 6 11 0 0.00 0.00 - no Open
306 3.6497166880267495 -0.682189 -21.9533 10 8 7 0.88 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 -21.953kcal/mol
Ligand efficiency (LE) -0.7840kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.402
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.29
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 72.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 122.96kcal/mol
Minimised FF energy 50.68kcal/mol

SASA & burial

✓ computed
SASA (unbound) 633.5Ų
Total solvent-accessible surface area of free ligand
BSA total 317.7Ų
Buried surface area upon binding
BSA apolar 208.4Ų
Hydrophobic contacts buried
BSA polar 109.3Ų
Polar contacts buried
Fraction buried 50.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3065.9Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1464.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)