FAIRMol

Z275025498

Pose ID 13264 Compound 760 Pose 385

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 Z275025498
PDB9IFH↗

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
12.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Burial
57%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.871 kcal/mol/HA) ✓ Good fit quality (FQ -8.22) ✓ Strong H-bond network (8 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Moderate strain (12.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-24.379
kcal/mol
LE
-0.871
kcal/mol/HA
Fit Quality
-8.22
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
3.57
cLogP
Strain ΔE
12.5 kcal/mol
SASA buried
57%
Lipo contact
65% BSA apolar/total
SASA unbound
653 Ų
Apolar buried
241 Ų

Interaction summary

HB 8 HY 11 PI 1 CLASH 4

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 rank4.557Score-24.379
Inter norm-0.781Intra norm-0.089
Top1000noExcludedno
Contacts11H-bonds8
Artifact reasongeometry warning; 11 clashes; 3 protein clashes
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 LYS410 PHE396 PRO398 SER395 THR397 THR463

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 overlap6Native recall0.75
Jaccard0.46RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
381 0.4678678754036258 -1.1526 -33.9568 4 15 0 0.00 0.00 - no Open
360 0.5197055751298865 -0.90829 -27.5829 3 17 0 0.00 0.00 - no Open
447 1.219696433124539 -0.981399 -29.5048 3 18 0 0.00 0.00 - no Open
355 1.3063524923317955 -1.04791 -30.2735 11 20 0 0.00 0.00 - no Open
408 1.743798155616244 -1.05333 -31.9361 3 16 0 0.00 0.00 - no Open
329 1.7650189558589326 -1.04283 -32.4787 6 12 0 0.00 0.00 - no Open
379 1.969342891855111 -0.889133 -24.5333 2 11 0 0.00 0.00 - no Open
325 2.125064930305446 -1.21138 -36.9499 9 20 0 0.00 0.00 - no Open
370 2.6577378078182576 -0.783465 -23.9328 5 9 0 0.00 0.00 - no Open
401 2.8276500106851037 -0.751507 -24.4635 10 12 0 0.00 0.00 - no Open
339 3.4270672992810502 -0.865213 -25.4592 9 17 0 0.00 0.00 - no Open
388 3.555555808287048 -0.931199 -26.8835 15 17 0 0.00 0.00 - no Open
360 3.9357191430534906 -1.02887 -25.0561 14 17 0 0.00 0.00 - no Open
385 4.556515282102343 -0.781229 -24.3789 8 11 6 0.75 0.00 - 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 -24.379kcal/mol
Ligand efficiency (LE) -0.8707kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.219
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 429.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.57
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 12.04kcal/mol
Minimised FF energy -0.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 653.2Ų
Total solvent-accessible surface area of free ligand
BSA total 370.2Ų
Buried surface area upon binding
BSA apolar 240.9Ų
Hydrophobic contacts buried
BSA polar 129.3Ų
Polar contacts buried
Fraction buried 56.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2983.7Ų
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 1533.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)