FAIRMol

MK218

Pose ID 11155 Compound 2169 Pose 312

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand MK218
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 high Native mixed SASA done
Strain ΔE
17.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.24, H-bond role recall 0.00
Burial
78%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
1 protein-contact clashes 71% of hydrophobic surface is solvent-exposed (17/24 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 (-0.539 kcal/mol/HA) ✓ Good fit quality (FQ -5.25) ✓ Good H-bonds (3 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (17.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-16.700
kcal/mol
LE
-0.539
kcal/mol/HA
Fit Quality
-5.25
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.89
cLogP
Final rank
3.6488
rank score
Inter norm
-0.752
normalised
Contacts
19
H-bonds 7
Strain ΔE
17.7 kcal/mol
SASA buried
78%
Lipo contact
82% BSA apolar/total
SASA unbound
716 Ų
Apolar buried
458 Ų

Interaction summary

HBD 1 HBA 2 HY 6 PI 1 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.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap6Native recall0.50
Jaccard0.24RMSD-
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
259 2.186616249521787 -0.767138 -19.682 6 18 0 0.00 0.00 - no Open
249 2.4030765412283297 -0.909145 -25.0763 5 13 0 0.00 0.00 - no Open
269 2.6372940514961205 -1.01685 -23.5396 9 22 0 0.00 0.00 - no Open
312 3.2393473524780756 -0.83684 -17.5204 10 15 0 0.00 0.00 - no Open
288 3.272332131596446 -0.77267 -17.6481 3 14 0 0.00 0.00 - no Open
312 3.6488397918246784 -0.752019 -16.7004 7 19 6 0.50 0.00 - no Current
266 3.7498473298653865 -0.798347 -21.5987 5 15 0 0.00 0.00 - no Open
288 4.113009301054676 -0.859307 -18.827 12 15 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 -16.700kcal/mol
Ligand efficiency (LE) -0.5387kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.248
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.89
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 47.07kcal/mol
Minimised FF energy 29.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 716.3Ų
Total solvent-accessible surface area of free ligand
BSA total 562.0Ų
Buried surface area upon binding
BSA apolar 457.8Ų
Hydrophobic contacts buried
BSA polar 104.2Ų
Polar contacts buried
Fraction buried 78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6604.4Ų
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 2066.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)