FAIRMol

MK179

Pose ID 13192 Compound 234 Pose 313

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 MK179
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
28.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.33, H-bond role recall 1.00
Burial
68%
Hydrophobic fit
61%
Reason: no major geometry red flags detected
2 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (7/20 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 (-0.585 kcal/mol/HA) ✓ Good fit quality (FQ -5.64) ✓ Good H-bonds (4 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (61%) ✗ High strain energy (28.6 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (10)
Score
-17.554
kcal/mol
LE
-0.585
kcal/mol/HA
Fit Quality
-5.64
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
2.66
cLogP
Strain ΔE
28.6 kcal/mol
SASA buried
68%
Lipo contact
61% BSA apolar/total
SASA unbound
707 Ų
Apolar buried
292 Ų

Interaction summary

HB 4 HY 15 PI 0 CLASH 2 ⚠ Exposure 35%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20 Buried (contacted) 13 Exposed 7 LogP 2.66 H-bonds 4
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank1.345Score-17.554
Inter norm-0.690Intra norm0.096
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 10 clashes; 5 protein contact clashes; moderate strain Δ 28.6
Residues
ARG472 GLU466 GLU467 HIS461 LEU399 MET393 MET400 MET471 PHE396 PRO398 PRO462 SER394 SER464 SER470 THR463 THR473

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
Jaccard0.33RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
258 0.25042243857344604 -1.14891 -31.0205 5 13 0 0.00 0.00 - no Open
264 1.0927050169268024 -1.00795 -24.7925 4 14 0 0.00 0.00 - no Open
235 1.1073660704846975 -0.900181 -23.0605 5 17 0 0.00 0.00 - no Open
257 1.107384658545134 -0.819468 -19.7407 2 17 0 0.00 0.00 - no Open
313 1.3452488083914984 -0.690473 -17.5537 4 16 6 0.75 1.00 - no Current
252 1.4292786430260862 -0.917081 -25.3234 6 21 0 0.00 0.00 - no Open
330 1.622607140224942 -0.920565 -25.7973 2 18 0 0.00 0.00 - no Open
281 1.8373311043657956 -0.808595 -21.8267 3 15 0 0.00 0.00 - no Open
206 1.8644199550012546 -0.798056 -18.2624 8 14 0 0.00 0.00 - no Open
361 2.311042942916434 -0.848092 -25.1719 4 12 0 0.00 0.00 - no Open
261 2.5727308749693383 -0.803338 -20.2039 2 12 0 0.00 0.00 - no Open
224 2.7169060620044525 -1.02158 -27.5832 9 18 0 0.00 0.00 - no Open
234 3.995775267533372 -1.22318 -34.5475 13 21 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 -17.554kcal/mol
Ligand efficiency (LE) -0.5851kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.644
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.66
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 77.34kcal/mol
Minimised FF energy 48.71kcal/mol

SASA & burial

✓ computed
SASA (unbound) 707.3Ų
Total solvent-accessible surface area of free ligand
BSA total 479.0Ų
Buried surface area upon binding
BSA apolar 292.2Ų
Hydrophobic contacts buried
BSA polar 186.8Ų
Polar contacts buried
Fraction buried 67.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3053.7Ų
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 1488.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)