FAIRMol

Z49712358

Pose ID 11414 Compound 3423 Pose 571

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z49712358
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
19.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.37, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.182 kcal/mol/HA) ✓ Good fit quality (FQ -10.08) ✓ Good H-bonds (4 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (19.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-24.820
kcal/mol
LE
-1.182
kcal/mol/HA
Fit Quality
-10.08
FQ (Leeson)
HAC
21
heavy atoms
MW
277
Da
LogP
3.78
cLogP
Strain ΔE
19.2 kcal/mol
SASA buried
82%
Lipo contact
89% BSA apolar/total
SASA unbound
523 Ų
Apolar buried
384 Ų

Interaction summary

HB 4 HY 23 PI 2 CLASH 2

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 rank2.094Score-24.820
Inter norm-1.070Intra norm-0.112
Top1000noExcludedno
Contacts14H-bonds4
Artifact reasongeometry warning; 13 clashes; 1 protein clash
Residues
ALA284 ALA365 ARG287 GLY197 GLY286 ILE199 LEU227 LEU332 LEU334 PHE198 PHE230 SER200 SER364 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 overlap7Native recall0.58
Jaccard0.37RMSD-
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
571 2.0935925308309 -1.06981 -24.8203 4 14 7 0.58 0.00 - no Current
575 2.5837901059382946 -1.03463 -24.0075 5 14 0 0.00 0.00 - no Open
545 2.674304460927894 -1.13412 -26.138 7 13 0 0.00 0.00 - no Open
575 3.1841179957797565 -1.13473 -22.6938 4 11 0 0.00 0.00 - no Open
567 4.607903799469551 -1.16439 -21.1887 7 14 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 -24.820kcal/mol
Ligand efficiency (LE) -1.1819kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.081
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 277.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.78
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 101.41kcal/mol
Minimised FF energy 82.21kcal/mol

SASA & burial

✓ computed
SASA (unbound) 523.0Ų
Total solvent-accessible surface area of free ligand
BSA total 430.2Ų
Buried surface area upon binding
BSA apolar 383.7Ų
Hydrophobic contacts buried
BSA polar 46.5Ų
Polar contacts buried
Fraction buried 82.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6487.0Ų
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 2052.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)