FAIRMol

Z56940509

Pose ID 11397 Compound 213 Pose 554

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 Z56940509
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
16.9 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.67, Jaccard 0.36, H-bond role recall 0.00
Burial
80%
Hydrophobic fit
76%
Reason: 12 internal clashes
12 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.656 kcal/mol/HA) ✓ Good fit quality (FQ -6.26) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (16.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-19.028
kcal/mol
LE
-0.656
kcal/mol/HA
Fit Quality
-6.26
FQ (Leeson)
HAC
29
heavy atoms
MW
400
Da
LogP
4.87
cLogP
Strain ΔE
16.9 kcal/mol
SASA buried
80%
Lipo contact
76% BSA apolar/total
SASA unbound
640 Ų
Apolar buried
390 Ų

Interaction summary

HB 5 HY 22 PI 3 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 rank3.302Score-19.028
Inter norm-0.803Intra norm0.145
Top1000noExcludedno
Contacts18H-bonds5
Artifact reasongeometry warning; 12 clashes; 2 protein clashes
Residues
ALA284 ALA365 ARG287 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER200 SER364 TYR221 VAL366

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 overlap8Native recall0.67
Jaccard0.36RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
507 0.3771837984194203 -1.155 -31.9494 3 15 0 0.00 0.00 - no Open
519 1.4342819729042058 -0.92092 -23.3081 4 19 0 0.00 0.00 - no Open
560 1.5514926483220204 -0.959439 -26.5577 5 14 0 0.00 0.00 - no Open
555 1.8654263966149012 -0.959208 -25.9063 5 14 0 0.00 0.00 - no Open
517 2.2213547153832276 -1.09021 -31.3015 6 20 0 0.00 0.00 - no Open
542 2.9002439451927176 -1.01929 -27.9611 5 18 0 0.00 0.00 - no Open
525 2.9778557631848654 -1.02688 -28.0687 5 14 0 0.00 0.00 - no Open
554 3.3019464620203967 -0.802515 -19.0283 5 18 8 0.67 0.00 - no Current
520 3.975288682413952 -0.927826 -24.4524 7 17 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 -19.028kcal/mol
Ligand efficiency (LE) -0.6561kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.263
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.87
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 18.94kcal/mol
Minimised FF energy 2.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 640.1Ų
Total solvent-accessible surface area of free ligand
BSA total 512.8Ų
Buried surface area upon binding
BSA apolar 390.5Ų
Hydrophobic contacts buried
BSA polar 122.3Ų
Polar contacts buried
Fraction buried 80.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6505.1Ų
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 2069.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)