FAIRMol

TC487

Pose ID 4985 Compound 551 Pose 244

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
T08
T. brucei PTR1 T. brucei
Ligand TC487
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 high Native strong SASA done
Strain ΔE
19.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.40
Burial
89%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.138 kcal/mol/HA) ✓ Good fit quality (FQ -10.98) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (19.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-34.136
kcal/mol
LE
-1.138
kcal/mol/HA
Fit Quality
-10.98
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
3.96
cLogP
Strain ΔE
19.6 kcal/mol
SASA buried
89%
Lipo contact
82% BSA apolar/total
SASA unbound
690 Ų
Apolar buried
507 Ų

Interaction summary

HB 7 HY 24 PI 7 CLASH 2

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
Final rank1.949Score-34.136
Inter norm-1.203Intra norm0.065
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash
Residues
ARG14 ASP161 CYS168 LEU208 LEU209 LYS220 MET163 MET169 NAP301 PHE171 PHE97 PRO210 TRP221 TYR174 VAL206 HIS267

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 overlap12Native recall0.63
Jaccard0.52RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
231 0.6014207356700648 -1.25321 -34.8174 5 16 16 0.84 0.20 - no Open
279 0.8504988960722657 -0.894167 -21.6384 6 19 0 0.00 0.00 - no Open
236 1.3083528962839743 -1.11776 -29.9104 4 16 14 0.74 0.20 - no Open
240 1.6299506770483856 -1.36717 -33.9407 4 17 14 0.74 0.20 - no Open
220 1.907698405551547 -0.951242 -21.9792 5 12 0 0.00 0.00 - no Open
244 1.9490770946923228 -1.20293 -34.136 7 16 12 0.63 0.40 - no Current
169 1.9707547428552354 -1.00186 -25.4722 8 19 0 0.00 0.00 - no Open
180 2.5014619286579576 -1.01708 -28.624 12 21 0 0.00 0.00 - no Open
264 2.7503390295192998 -0.880821 -21.3824 8 15 0 0.00 0.00 - no Open
165 2.77418758404451 -0.994655 -25.2548 10 17 0 0.00 0.00 - no Open
364 2.8667019787780563 -0.791058 -20.2445 7 10 0 0.00 0.00 - no Open
197 2.867821243861192 -1.03605 -27.4804 4 17 0 0.00 0.00 - no Open
309 3.2254665102249094 -0.900419 -26.4298 4 19 0 0.00 0.00 - no Open
228 3.4221328759899046 -0.818918 -19.4455 6 13 0 0.00 0.00 - no Open
190 3.711702843008295 -1.02661 -29.2265 10 20 0 0.00 0.00 - no Open
336 3.838572716904155 -0.771486 -20.5454 6 13 0 0.00 0.00 - no Open
372 4.383389719759655 -0.920685 -23.3789 10 11 0 0.00 0.00 - no Open
258 4.612847442136598 -0.816328 -20.9905 6 18 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 -34.136kcal/mol
Ligand efficiency (LE) -1.1379kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.976
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.96
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 85.18kcal/mol
Minimised FF energy 65.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 690.2Ų
Total solvent-accessible surface area of free ligand
BSA total 614.7Ų
Buried surface area upon binding
BSA apolar 506.5Ų
Hydrophobic contacts buried
BSA polar 108.1Ų
Polar contacts buried
Fraction buried 89.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1691.8Ų
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 922.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)