FAIRMol

TC369

Pose ID 4977 Compound 551 Pose 236

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 TC369
PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
23.8 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.20
Burial
86%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.997 kcal/mol/HA) ✓ Good fit quality (FQ -9.62) ✓ Good H-bonds (4 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (23.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (14)
Score
-29.910
kcal/mol
LE
-0.997
kcal/mol/HA
Fit Quality
-9.62
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
3.96
cLogP
Strain ΔE
23.8 kcal/mol
SASA buried
86%
Lipo contact
81% BSA apolar/total
SASA unbound
692 Ų
Apolar buried
478 Ų

Interaction summary

HB 4 HY 24 PI 5 CLASH 3

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 rank1.308Score-29.910
Inter norm-1.118Intra norm0.121
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 14 clashes; 5 protein contact clashes; 5 cofactor-context clashes; moderate strain Δ 23.5
Residues
ARG14 ASP161 CYS168 LEU208 LEU209 MET169 MET213 NAP301 PHE171 PHE97 PRO210 SER95 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 overlap14Native recall0.74
Jaccard0.67RMSD-
HB strict2Strict recall0.33
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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 Current
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 Open
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 -29.910kcal/mol
Ligand efficiency (LE) -0.9970kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.617
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) 23.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 78.62kcal/mol
Minimised FF energy 54.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 692.3Ų
Total solvent-accessible surface area of free ligand
BSA total 591.6Ų
Buried surface area upon binding
BSA apolar 478.1Ų
Hydrophobic contacts buried
BSA polar 113.5Ų
Polar contacts buried
Fraction buried 85.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1682.2Ų
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 919.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)