FAIRMol

MK156

Pose ID 13189 Compound 1078 Pose 310

DB fairmolDocking 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 MK156
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
Likely artefact or unreliable pose
Binding strong Geometry high Native strong SASA done
Strain ΔE
20.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 0.00
Burial
59%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.637 kcal/mol/HA) ✓ Good fit quality (FQ -5.87) ✓ Good H-bonds (4 bonds) ✓ Good burial (59% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (20.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (12)
Score
-16.571
kcal/mol
LE
-0.637
kcal/mol/HA
Fit Quality
-5.87
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
2.95
cLogP
Final rank
1.5346
rank score
Inter norm
-0.726
normalised
Contacts
10
H-bonds 4
Strain ΔE
20.1 kcal/mol
SASA buried
59%
Lipo contact
74% BSA apolar/total
SASA unbound
596 Ų
Apolar buried
260 Ų

Interaction summary

HBD 1 HBA 3 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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

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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.50RMSD-
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
313 0.8712913457919358 -1.07999 -25.8552 3 16 0 0.00 0.00 - no Open
259 1.0887783330232708 -1.16095 -30.3355 8 18 0 0.00 0.00 - no Open
310 1.5345591015763724 -0.726221 -16.5713 4 10 6 0.75 0.00 - no Current
229 2.0704697110349266 -0.998736 -19.793 2 14 0 0.00 0.00 - no Open
256 2.3416472278121194 -1.03745 -25.3269 2 11 0 0.00 0.00 - no Open
245 2.6468222692756207 -1.26083 -33.0935 10 12 0 0.00 0.00 - no Open
191 3.0336689687352054 -1.09429 -28.6535 9 15 0 0.00 0.00 - no Open
277 3.806776809599375 -0.815034 -16.965 6 13 0 0.00 0.00 - no Open
214 3.8581501940359018 -1.22756 -28.0706 10 18 0 0.00 0.00 - no Open
297 3.8864053339831193 -0.911524 -23.3962 3 13 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 -16.571kcal/mol
Ligand efficiency (LE) -0.6374kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.872
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.95
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 50.62kcal/mol
Minimised FF energy 30.55kcal/mol

SASA & burial

✓ computed
SASA (unbound) 596.0Ų
Total solvent-accessible surface area of free ligand
BSA total 351.6Ų
Buried surface area upon binding
BSA apolar 259.8Ų
Hydrophobic contacts buried
BSA polar 91.8Ų
Polar contacts buried
Fraction buried 59.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2980.1Ų
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 1531.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)