FAIRMol

Z56804221

Pose ID 13328 Compound 5236 Pose 449

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 Z56804221
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 high Native strong SASA done
Strain ΔE
19.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 1.00
Burial
54%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
1 protein-contact clashes 38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.483 kcal/mol/HA) ✓ Good fit quality (FQ -4.66) ✓ Good H-bonds (4 bonds) ✓ Good burial (54% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (19.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-14.503
kcal/mol
LE
-0.483
kcal/mol/HA
Fit Quality
-4.66
FQ (Leeson)
HAC
30
heavy atoms
MW
402
Da
LogP
4.24
cLogP
Strain ΔE
19.2 kcal/mol
SASA buried
54%
Lipo contact
85% BSA apolar/total
SASA unbound
714 Ų
Apolar buried
330 Ų

Interaction summary

HB 4 HY 20 PI 1 CLASH 1 ⚠ Exposure 37%

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
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24 Buried (contacted) 15 Exposed 9 LogP 4.24 H-bonds 4
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank2.829Score-14.503
Inter norm-0.654Intra norm0.170
Top1000noExcludedno
Contacts9H-bonds4
Artifact reasongeometry warning; 15 clashes; 1 protein clash
Residues
ASN402 GLU467 LEU399 LYS407 MET400 PHE396 PRO398 PRO462 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 overlap6Native recall0.75
Jaccard0.55RMSD-
HB strict1Strict recall0.50
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
449 2.8287208373760326 -0.653876 -14.5027 4 9 6 0.75 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 -14.503kcal/mol
Ligand efficiency (LE) -0.4834kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.663
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 402.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.24
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 100.43kcal/mol
Minimised FF energy 81.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 714.1Ų
Total solvent-accessible surface area of free ligand
BSA total 386.1Ų
Buried surface area upon binding
BSA apolar 329.8Ų
Hydrophobic contacts buried
BSA polar 56.3Ų
Polar contacts buried
Fraction buried 54.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3146.2Ų
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 1518.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)