FAIRMol

Z25044315

Pose ID 13389 Compound 1657 Pose 510

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand Z25044315
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
18.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Burial
56%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
1 protein-contact clashes 56% of hydrophobic surface appears solvent-exposed (9/16 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 (-0.678 kcal/mol/HA) ✓ Good fit quality (FQ -6.08) ✓ Good H-bonds (5 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (18.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-16.281
kcal/mol
LE
-0.678
kcal/mol/HA
Fit Quality
-6.08
FQ (Leeson)
HAC
24
heavy atoms
MW
385
Da
LogP
4.28
cLogP
Strain ΔE
18.3 kcal/mol
SASA buried
56%
Lipo contact
85% BSA apolar/total
SASA unbound
599 Ų
Apolar buried
288 Ų

Interaction summary

HB 5 HY 10 PI 1 CLASH 1 ⚠ Exposure 56%

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
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16 Buried (contacted) 7 Exposed 9 LogP 4.28 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.131Score-16.281
Inter norm-0.787Intra norm0.108
Top1000noExcludedno
Contacts11H-bonds5
Artifact reasongeometry warning; 11 clashes; 1 protein clash
Residues
ASN402 GLU466 GLU467 LEU399 LYS407 LYS410 PHE396 PRO398 SER464 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
517 0.4246347756871142 -1.02311 -25.3137 0 12 0 0.00 0.00 - no Open
491 1.7835069759055122 -1.19134 -28.1663 3 14 0 0.00 0.00 - no Open
510 2.1310929517662007 -0.786782 -16.2806 5 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 -16.281kcal/mol
Ligand efficiency (LE) -0.6784kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.079
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 385.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.28
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 85.88kcal/mol
Minimised FF energy 67.59kcal/mol

SASA & burial

✓ computed
SASA (unbound) 598.6Ų
Total solvent-accessible surface area of free ligand
BSA total 338.4Ų
Buried surface area upon binding
BSA apolar 287.8Ų
Hydrophobic contacts buried
BSA polar 50.5Ų
Polar contacts buried
Fraction buried 56.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3031.7Ų
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 1529.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)