FAIRMol

MK153

Pose ID 9869 Compound 2730 Pose 383

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand MK153
PDB9IFF↗

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 mixed SASA done
Strain ΔE
15.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.54, Jaccard 0.44
Burial
58%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.691 kcal/mol/HA) ✓ Good fit quality (FQ -6.66) ✓ Strong H-bond network (8 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (15.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-20.717
kcal/mol
LE
-0.691
kcal/mol/HA
Fit Quality
-6.66
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
4.74
cLogP
Strain ΔE
15.5 kcal/mol
SASA buried
58%
Lipo contact
77% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
310 Ų

Interaction summary

HB 8 HY 18 PI 0 CLASH 4

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
Final rank2.966Score-20.717
Inter norm-0.817Intra norm0.127
Top1000noExcludedno
Contacts10H-bonds8
Artifact reasongeometry warning; 11 clashes; 1 protein clash
Residues
ARG74 ASN245 ASP71 GLY214 GLY215 LYS211 LYS89 MET70 PRO212 PRO213

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap7Native recall0.54
Jaccard0.44RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
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:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
256 0.31638489365544653 -1.29672 -32.318 6 16 0 0.00 - - no Open
253 1.8534100571059364 -1.09083 -28.6922 14 11 0 0.00 - - no Open
188 2.335241481496056 -1.05817 -27.7995 9 18 0 0.00 - - no Open
226 2.797223121583977 -1.02004 -25.9723 4 17 0 0.00 - - no Open
383 2.9656784107887395 -0.817119 -20.7174 8 10 7 0.54 - - no Current
357 3.111077451899158 -0.759397 -21.5499 5 14 0 0.00 - - no Open
250 3.9521264673394088 -0.950188 -22.7349 7 19 0 0.00 - - no Open
272 4.149605552322236 -1.01476 -26.5406 10 16 0 0.00 - - no Open
202 4.363632399401475 -1.00063 -24.108 9 18 0 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 -20.717kcal/mol
Ligand efficiency (LE) -0.6906kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.662
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.74
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 47.37kcal/mol
Minimised FF energy 31.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.8Ų
Total solvent-accessible surface area of free ligand
BSA total 402.9Ų
Buried surface area upon binding
BSA apolar 309.6Ų
Hydrophobic contacts buried
BSA polar 93.3Ų
Polar contacts buried
Fraction buried 58.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3037.6Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1551.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)