FAIRMol

Z56765335

Pose ID 11338 Compound 1212 Pose 495

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z56765335
PDB5S9T↗

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 high Native strong SASA done
Strain ΔE
23.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.33, H-bond role recall 0.00
Burial
85%
Hydrophobic fit
87%
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 (-0.831 kcal/mol/HA) ✓ Good fit quality (FQ -7.84) ✓ Good H-bonds (3 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ High strain energy (23.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-23.253
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-7.84
FQ (Leeson)
HAC
28
heavy atoms
MW
374
Da
LogP
2.71
cLogP
Strain ΔE
23.0 kcal/mol
SASA buried
85%
Lipo contact
87% BSA apolar/total
SASA unbound
662 Ų
Apolar buried
490 Ų

Interaction summary

HB 3 HY 19 PI 2 CLASH 1
Final rank2.028Score-23.253
Inter norm-0.816Intra norm-0.014
Top1000noExcludedno
Contacts16H-bonds3
Artifact reasongeometry warning; 10 clashes; 1 protein clash; moderate strain Δ 23.0
Residues
ALA284 ALA363 ARG287 CYS375 GLY197 GLY286 GLY376 ILE199 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL362

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap7Native recall0.58
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
477 1.9185062916126276 -0.954005 -25.6366 5 16 0 0.00 0.00 - no Open
495 2.0281070354192057 -0.815998 -23.2531 3 16 7 0.58 0.00 - no Current
436 3.47512672009095 -1.11523 -30.328 14 16 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 -23.253kcal/mol
Ligand efficiency (LE) -0.8305kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.840
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.71
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 48.07kcal/mol
Minimised FF energy 25.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 661.9Ų
Total solvent-accessible surface area of free ligand
BSA total 564.0Ų
Buried surface area upon binding
BSA apolar 489.9Ų
Hydrophobic contacts buried
BSA polar 74.2Ų
Polar contacts buried
Fraction buried 85.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6549.0Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2086.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)