FAIRMol

MK216

Pose ID 7686 Compound 741 Pose 234

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
T12
T. brucei R5P T. brucei
Ligand MK216
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
28.6 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.94, Jaccard 0.71, H-bond role recall 0.40
Burial
80%
Hydrophobic fit
80%
Reason: 12 internal clashes
12 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.980 kcal/mol/HA) ✓ Good fit quality (FQ -9.46) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (28.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-29.408
kcal/mol
LE
-0.980
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
28.6 kcal/mol
SASA buried
80%
Lipo contact
80% BSA apolar/total
SASA unbound
682 Ų
Apolar buried
436 Ų

Interaction summary

HB 12 HY 12 PI 4 CLASH 0

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

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank3.409Score-29.408
Inter norm-1.092Intra norm0.112
Top1000noExcludedno
Contacts20H-bonds12
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; moderate strain Δ 28.6
Residues
ARG140 ARG144 ASN106 GLN104 HIS105 HIS141 MET101 TYR97 ARG116 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 MET78 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap15Native recall0.94
Jaccard0.71RMSD-
HB strict4Strict recall0.33
HB same residue+role4HB role recall0.40
HB same residue5HB residue recall0.50

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
270 0.41464125782172895 -1.24727 -30.931 5 18 0 0.00 0.00 - no Open
254 0.6988781872574225 -1.25188 -32.2522 4 18 0 0.00 0.00 - no Open
251 0.7250052548167374 -1.13109 -29.7477 9 16 0 0.00 0.00 - no Open
261 1.0426509139693059 -1.20512 -33.9388 8 16 0 0.00 0.00 - no Open
325 1.1123859942003849 -0.870106 -23.9953 5 17 0 0.00 0.00 - no Open
284 1.2799241570993618 -0.701211 -16.1709 2 15 0 0.00 0.00 - no Open
261 2.1714771596576723 -0.876999 -24.0478 4 20 0 0.00 0.00 - no Open
242 2.173345721097384 -0.939642 -26.2628 3 17 0 0.00 0.00 - no Open
268 2.258376845222224 -1.34754 -36.7611 6 18 0 0.00 0.00 - no Open
286 2.455516370069698 -0.756571 -20.7825 5 16 0 0.00 0.00 - no Open
231 2.507441772388101 -0.993468 -27.2209 10 16 15 0.94 0.60 - no Open
388 2.646525773858347 -0.921618 -24.6948 7 9 0 0.00 0.00 - no Open
310 3.2694404438220586 -0.809948 -22.0335 6 20 0 0.00 0.00 - no Open
382 3.283984438521126 -0.790489 -19.8104 10 13 0 0.00 0.00 - no Open
207 3.3094615427951894 -1.10423 -30.2339 10 20 0 0.00 0.00 - no Open
234 3.409408458633953 -1.09234 -29.4077 12 20 15 0.94 0.40 - no Current
245 3.4162752319055487 -0.920939 -25.2102 5 18 0 0.00 0.00 - no Open
310 3.5161728665857086 -0.795591 -22.0764 7 13 0 0.00 0.00 - no Open
391 3.596788774445806 -0.962215 -24.9581 7 10 0 0.00 0.00 - no Open
187 3.6651296797272988 -1.08872 -28.1762 10 20 0 0.00 0.00 - no Open
308 3.819364771089957 -0.792144 -21.3443 5 18 0 0.00 0.00 - no Open
264 3.966830308384504 -0.853893 -24.9405 6 14 0 0.00 0.00 - no Open
286 4.439393815944125 -0.990465 -24.6013 12 19 0 0.00 0.00 - no Open
283 4.505496780270578 -0.967133 -27.3864 10 16 0 0.00 0.00 - no Open
290 4.658138957438228 -0.76781 -20.3267 6 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 -29.408kcal/mol
Ligand efficiency (LE) -0.9803kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.456
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.89kcal/mol
Minimised FF energy 25.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 681.9Ų
Total solvent-accessible surface area of free ligand
BSA total 546.8Ų
Buried surface area upon binding
BSA apolar 435.6Ų
Hydrophobic contacts buried
BSA polar 111.2Ų
Polar contacts buried
Fraction buried 80.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2242.0Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 774.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)