FAIRMol

TC483

Pose ID 7640 Compound 3161 Pose 188

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
T12
T. brucei R5P T. brucei
Ligand TC483
PDB6FXS↗

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
31.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.81, Jaccard 0.65, H-bond role recall 0.30
Burial
60%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 69% of hydrophobic surface is solvent-exposed (22/32 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.592 kcal/mol/HA) ✓ Good fit quality (FQ -6.22) ✓ Strong H-bond network (10 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Very high strain energy (31.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-24.276
kcal/mol
LE
-0.592
kcal/mol/HA
Fit Quality
-6.22
FQ (Leeson)
HAC
41
heavy atoms
MW
559
Da
LogP
5.24
cLogP
Strain ΔE
31.7 kcal/mol
SASA buried
60%
Lipo contact
83% BSA apolar/total
SASA unbound
917 Ų
Apolar buried
454 Ų

Interaction summary

HB 10 HY 9 PI 2 CLASH 4 ⚠ Exposure 68%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
69% of hydrophobic surface is solvent-exposed (22/32 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 32 Buried (contacted) 10 Exposed 22 LogP 5.24 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (8 atoms exposed)
Final rank4.268Score-24.276
Inter norm-0.742Intra norm0.150
Top1000noExcludedno
Contacts17H-bonds10
Artifact reasongeometry warning; 18 clashes; 1 protein clash; high strain Δ 31.1
Residues
ALA102 ARG140 ARG144 ASN106 HIS105 HIS141 MET101 TYR97 ARG116 ARG46 CYS72 GLY73 GLY77 HIS14 ILE15 ILE76 SER74

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap13Native recall0.81
Jaccard0.65RMSD-
HB strict3Strict recall0.25
HB same residue+role3HB role recall0.30
HB same residue4HB residue recall0.40

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
243 3.7127852995163635 -0.780171 -25.6506 6 16 0 0.00 0.00 - no Open
188 4.2676262282320385 -0.741775 -24.2765 10 17 13 0.81 0.30 - no Current
208 4.51709479773615 -0.64753 -17.8777 5 19 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -24.276kcal/mol
Ligand efficiency (LE) -0.5921kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.222
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 41HA

Physicochemical properties
Molecular weight 558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.24
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 145.60kcal/mol
Minimised FF energy 113.95kcal/mol

SASA & burial

✓ computed
SASA (unbound) 916.6Ų
Total solvent-accessible surface area of free ligand
BSA total 547.3Ų
Buried surface area upon binding
BSA apolar 454.1Ų
Hydrophobic contacts buried
BSA polar 93.2Ų
Polar contacts buried
Fraction buried 59.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2433.6Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 817.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)