FAIRMol

MK216

Pose ID 8337 Compound 741 Pose 207

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand MK216
PDB1F3T↗

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
30.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.43
Burial
80%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.008 kcal/mol/HA) ✓ Good fit quality (FQ -9.72) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (30.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-30.234
kcal/mol
LE
-1.008
kcal/mol/HA
Fit Quality
-9.72
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
30.2 kcal/mol
SASA buried
80%
Lipo contact
79% BSA apolar/total
SASA unbound
630 Ų
Apolar buried
398 Ų

Interaction summary

HB 10 HY 6 PI 4 CLASH 1

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
Final rank3.309Score-30.234
Inter norm-1.104Intra norm0.096
Top1000noExcludedno
Contacts20H-bonds10
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; high strain Δ 30.2
Residues
ALA67 ARG154 ARG277 ASP158 ASP88 GLU274 GLY199 GLY201 GLY236 GLY237 GLY276 HIS197 LYS69 PHE170 PHE238 PRO275 SER200 TYR278 TYR389 VAL198

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap15Native recall0.79
Jaccard0.62RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

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 0 0.00 0.00 - 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 1 0.05 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 15 0.79 0.43 - no Current
234 3.409408458633953 -1.09234 -29.4077 12 20 0 0.00 0.00 - no Open
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 15 0.79 0.57 - no Open
308 3.819364771089957 -0.792144 -21.3443 5 18 1 0.05 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 1 0.05 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 -30.234kcal/mol
Ligand efficiency (LE) -1.0078kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.722
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) 30.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 55.51kcal/mol
Minimised FF energy 25.32kcal/mol

SASA & burial

✓ computed
SASA (unbound) 630.0Ų
Total solvent-accessible surface area of free ligand
BSA total 502.1Ų
Buried surface area upon binding
BSA apolar 397.7Ų
Hydrophobic contacts buried
BSA polar 104.4Ų
Polar contacts buried
Fraction buried 79.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2579.4Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1393.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)