FAIRMol

MK61

Pose ID 13184 Compound 919 Pose 305

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 MK61
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
56.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.40, H-bond role recall 0.00
Burial
53%
Hydrophobic fit
87%
Reason: strain 56.3 kcal/mol
strain ΔE 56.3 kcal/mol 2 protein-contact clashes 52% of hydrophobic surface appears solvent-exposed (15/29 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 (-0.523 kcal/mol/HA) ✓ Good fit quality (FQ -5.32) ✓ Good H-bonds (4 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Extreme strain energy (56.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-18.841
kcal/mol
LE
-0.523
kcal/mol/HA
Fit Quality
-5.32
FQ (Leeson)
HAC
36
heavy atoms
MW
496
Da
LogP
2.52
cLogP
Final rank
4.8872
rank score
Inter norm
-0.555
normalised
Contacts
13
H-bonds 6
Strain ΔE
56.3 kcal/mol
SASA buried
53%
Lipo contact
87% BSA apolar/total
SASA unbound
802 Ų
Apolar buried
368 Ų

Interaction summary

HBD 3 HBA 1 HY 4 PI 1 CLASH 2

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

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: permissive.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.40RMSD-
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
307 2.2909866787455915 -0.772941 -28.692 4 20 0 0.00 0.00 - no Open
288 2.3712549618822396 -0.708682 -22.3336 4 20 0 0.00 0.00 - no Open
305 4.887229888844244 -0.554716 -18.8415 6 13 6 0.75 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 -18.841kcal/mol
Ligand efficiency (LE) -0.5234kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.319
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 495.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.52
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 56.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 153.60kcal/mol
Minimised FF energy 97.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 802.1Ų
Total solvent-accessible surface area of free ligand
BSA total 422.6Ų
Buried surface area upon binding
BSA apolar 367.8Ų
Hydrophobic contacts buried
BSA polar 54.8Ų
Polar contacts buried
Fraction buried 52.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3276.6Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1497.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)