FAIRMol

TC391

Pose ID 4978 Compound 3114 Pose 237

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
T08
T. brucei PTR1 T. brucei
Ligand TC391
PDB6RX6↗

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
20.2 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.80
Burial
78%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes 43% of hydrophobic surface appears solvent-exposed (10/23 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 (-1.097 kcal/mol/HA) ✓ Good fit quality (FQ -10.58) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ High strain energy (20.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-32.894
kcal/mol
LE
-1.097
kcal/mol/HA
Fit Quality
-10.58
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
4.90
cLogP
Strain ΔE
20.2 kcal/mol
SASA buried
78%
Lipo contact
77% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
392 Ų

Interaction summary

HB 13 HY 16 PI 2 CLASH 3 ⚠ Exposure 43%

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
43% of hydrophobic surface appears solvent-exposed (10/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23 Buried (contacted) 13 Exposed 10 LogP 4.9 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank1.993Score-32.894
Inter norm-1.149Intra norm0.053
Top1000noExcludedno
Contacts13H-bonds13
Artifact reasongeometry warning; 13 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 20.2
Residues
ALA96 ARG14 ASN127 LEU208 LYS13 LYS178 NAP301 PHE97 PRO210 SER95 TYR174 TYR98 VAL211

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap9Native recall0.47
Jaccard0.39RMSD-
HB strict5Strict recall0.83
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
249 1.089440178396187 -0.844931 -21.6098 3 15 0 0.00 0.00 - no Open
237 1.9932837433636637 -1.14932 -32.894 13 13 9 0.47 0.80 - no Current
279 2.0643017699037225 -0.669226 -16.9623 6 13 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 -32.894kcal/mol
Ligand efficiency (LE) -1.0965kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.577
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 69.30kcal/mol
Minimised FF energy 49.07kcal/mol

SASA & burial

✓ computed
SASA (unbound) 650.0Ų
Total solvent-accessible surface area of free ligand
BSA total 507.9Ų
Buried surface area upon binding
BSA apolar 392.3Ų
Hydrophobic contacts buried
BSA polar 115.5Ų
Polar contacts buried
Fraction buried 78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1628.1Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 952.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)