FAIRMol

TC489

Pose ID 13799 Compound 1122 Pose 241

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
T21
T. cruzi R5P T. cruzi
Ligand TC489
PDB3K7O↗

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
30.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.67
Burial
59%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
2 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (15/30 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 (-0.778 kcal/mol/HA) ✓ Good fit quality (FQ -8.02) ✓ Strong H-bond network (15 bonds) ✓ Good burial (59% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (30.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-29.547
kcal/mol
LE
-0.778
kcal/mol/HA
Fit Quality
-8.02
FQ (Leeson)
HAC
38
heavy atoms
MW
516
Da
LogP
3.89
cLogP
Strain ΔE
30.5 kcal/mol
SASA buried
59%
Lipo contact
81% BSA apolar/total
SASA unbound
801 Ų
Apolar buried
382 Ų

Interaction summary

HB 15 HY 4 PI 4 CLASH 2 ⚠ Exposure 50%
⚠️Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (15/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30 Buried (contacted) 15 Exposed 15 LogP 3.89 H-bonds 15
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (7 atoms exposed)
Final rank5.349Score-29.547
Inter norm-0.725Intra norm-0.053
Top1000noExcludedno
Contacts16H-bonds15
Artifact reasongeometry warning; 16 clashes; 3 protein clashes; high strain Δ 30.5
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 CYS69 GLY70 GLY72 GLY74 HIS11 ILE73 PRO12 SER71 TYR46

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap13Native recall0.93
Jaccard0.76RMSD-
HB strict7Strict recall0.58
HB same residue+role6HB role recall0.67
HB same residue5HB residue recall0.62

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
291 1.4078249954263844 -0.767107 -30.4751 5 20 0 0.00 0.00 - no Open
264 4.845218036863834 -0.602005 -20.5177 6 15 0 0.00 0.00 - no Open
241 5.349385339385592 -0.724881 -29.5472 15 16 13 0.93 0.67 - 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 -29.547kcal/mol
Ligand efficiency (LE) -0.7776kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.016
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 515.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.89
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 111.04kcal/mol
Minimised FF energy 80.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 801.2Ų
Total solvent-accessible surface area of free ligand
BSA total 470.3Ų
Buried surface area upon binding
BSA apolar 381.6Ų
Hydrophobic contacts buried
BSA polar 88.7Ų
Polar contacts buried
Fraction buried 58.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2388.6Ų
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 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 787.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)