FAIRMol

MK27

Pose ID 11127 Compound 3572 Pose 284

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 MK27
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 medium Native strong SASA done
Strain ΔE
37.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.83, Jaccard 0.53, H-bond role recall 0.00
Burial
74%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.538 kcal/mol/HA) ✓ Good fit quality (FQ -5.47) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (37.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-19.361
kcal/mol
LE
-0.538
kcal/mol/HA
Fit Quality
-5.47
FQ (Leeson)
HAC
36
heavy atoms
MW
519
Da
LogP
2.26
cLogP
Final rank
3.7039
rank score
Inter norm
-0.628
normalised
Contacts
17
H-bonds 4
Strain ΔE
37.5 kcal/mol
SASA buried
74%
Lipo contact
81% BSA apolar/total
SASA unbound
826 Ų
Apolar buried
499 Ų

Interaction summary

HBD 2 HBA 1 HY 7 PI 1 CLASH 3

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 overlap10Native recall0.83
Jaccard0.53RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

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
353 2.925637514091269 -0.674099 -21.9374 4 18 0 0.00 0.00 - no Open
284 3.7038824639745087 -0.628274 -19.3613 4 17 10 0.83 0.00 - no Current
188 5.102161794543185 -0.687821 -14.4168 13 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 -19.361kcal/mol
Ligand efficiency (LE) -0.5378kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.466
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 518.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.26
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 124.19kcal/mol
Minimised FF energy 86.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 826.2Ų
Total solvent-accessible surface area of free ligand
BSA total 613.5Ų
Buried surface area upon binding
BSA apolar 499.3Ų
Hydrophobic contacts buried
BSA polar 114.2Ų
Polar contacts buried
Fraction buried 74.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6705.8Ų
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 2061.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)