FAIRMol

NMT-TY0623

Pose ID 9910 Compound 343 Pose 424

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand NMT-TY0623
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 strong SASA done
Strain ΔE
38.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.50
Burial
69%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 47% of hydrophobic surface appears solvent-exposed (9/19 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 (-0.972 kcal/mol/HA) ✓ Good fit quality (FQ -9.28) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (38.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-28.189
kcal/mol
LE
-0.972
kcal/mol/HA
Fit Quality
-9.28
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.54
cLogP
Strain ΔE
38.7 kcal/mol
SASA buried
69%
Lipo contact
72% BSA apolar/total
SASA unbound
704 Ų
Apolar buried
350 Ų

Interaction summary

HB 8 HY 19 PI 1 CLASH 3 ⚠ Exposure 47%
⚠️Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 10 Exposed 9 LogP 2.54 H-bonds 8
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank2.557Score-28.189
Inter norm-0.989Intra norm0.016
Top1000noExcludedno
Contacts17H-bonds8
Artifact reasongeometry warning; 11 clashes; 1 protein clash; high strain Δ 38.7
Residues
ALA209 ALA67 ALA90 ASN208 GLY214 GLY215 GLY66 LEU73 LYS211 LYS216 LYS89 MET70 PRO212 PRO213 TYR210 TYR69 VAL88

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

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 overlap10Native recall0.77
Jaccard0.50RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 - - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 0 0.00 - - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 - - no Open
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 - - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 0 0.00 - - no Open
424 2.557044498817305 -0.988533 -28.1895 8 17 10 0.77 - - no Current
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 - - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 - - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 - - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 - - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 0 0.00 - - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 0 0.00 - - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 0 0.00 - - no Open
289 3.87862843107247 -0.963867 -29.2468 8 19 0 0.00 - - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 0 0.00 - - no Open
309 4.286815840501966 -0.801912 -23.8944 5 20 0 0.00 - - no Open
269 4.88188196770325 -1.1395 -32.34 11 17 0 0.00 - - no Open
255 5.815034729044303 -0.891682 -22.7371 13 16 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 -28.189kcal/mol
Ligand efficiency (LE) -0.9721kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.279
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.54
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -71.43kcal/mol
Minimised FF energy -110.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 703.9Ų
Total solvent-accessible surface area of free ligand
BSA total 484.5Ų
Buried surface area upon binding
BSA apolar 350.1Ų
Hydrophobic contacts buried
BSA polar 134.3Ų
Polar contacts buried
Fraction buried 68.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2989.0Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1550.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)