FAIRMol

Z56857258

Pose ID 13333 Compound 5204 Pose 454

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z56857258
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Burial
58%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.685 kcal/mol/HA) ✓ Good fit quality (FQ -6.80) ✓ Strong H-bond network (6 bonds) ✓ Good burial (58% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Moderate strain (19.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-22.602
kcal/mol
LE
-0.685
kcal/mol/HA
Fit Quality
-6.80
FQ (Leeson)
HAC
33
heavy atoms
MW
462
Da
LogP
5.13
cLogP
Strain ΔE
19.0 kcal/mol
SASA buried
58%
Lipo contact
88% BSA apolar/total
SASA unbound
730 Ų
Apolar buried
372 Ų

Interaction summary

HB 6 HY 24 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 rank2.143Score-22.602
Inter norm-0.571Intra norm-0.114
Top1000noExcludedno
Contacts12H-bonds6
Artifact reasongeometry warning; 5 clashes; 1 protein clash
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 MET393 MET471 PHE396 PRO398 SER394 SER470 THR397

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.67RMSD-
HB strict2Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
454 2.1427130310360645 -0.570621 -22.6023 6 12 8 1.00 1.00 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -22.602kcal/mol
Ligand efficiency (LE) -0.6849kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.796
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.13
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 47.70kcal/mol
Minimised FF energy 28.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 729.8Ų
Total solvent-accessible surface area of free ligand
BSA total 425.3Ų
Buried surface area upon binding
BSA apolar 372.2Ų
Hydrophobic contacts buried
BSA polar 53.1Ų
Polar contacts buried
Fraction buried 58.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3161.1Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1515.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)