FAIRMol

TC483

Pose ID 4984 Compound 3161 Pose 243

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 TC483
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
53.5 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.40
Burial
75%
Hydrophobic fit
88%
Reason: strain 53.5 kcal/mol
strain ΔE 53.5 kcal/mol
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.626 kcal/mol/HA) ✓ Good fit quality (FQ -6.57) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Extreme strain energy (53.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-25.651
kcal/mol
LE
-0.626
kcal/mol/HA
Fit Quality
-6.57
FQ (Leeson)
HAC
41
heavy atoms
MW
559
Da
LogP
5.24
cLogP
Strain ΔE
53.5 kcal/mol
SASA buried
75%
Lipo contact
88% BSA apolar/total
SASA unbound
855 Ų
Apolar buried
567 Ų

Interaction summary

HB 6 HY 24 PI 3 CLASH 1

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 rank3.713Score-25.651
Inter norm-0.780Intra norm0.155
Top1000noExcludedno
Contacts16H-bonds6
Artifact reasongeometry warning; 19 clashes; 2 protein clashes; 2 cofactor-context clashes; high strain Δ 52.8
Residues
ALA212 ALA96 ARG14 CYS168 GLU217 LEU208 LEU209 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER95 TRP221 TYR98

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 overlap13Native recall0.68
Jaccard0.59RMSD-
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
243 3.7127852995163635 -0.780171 -25.6506 6 16 13 0.68 0.40 - no Current
188 4.2676262282320385 -0.741775 -24.2765 10 17 0 0.00 0.00 - no Open
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 -25.651kcal/mol
Ligand efficiency (LE) -0.6256kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.574
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) 53.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 160.44kcal/mol
Minimised FF energy 106.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 855.0Ų
Total solvent-accessible surface area of free ligand
BSA total 642.7Ų
Buried surface area upon binding
BSA apolar 566.6Ų
Hydrophobic contacts buried
BSA polar 76.1Ų
Polar contacts buried
Fraction buried 75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1894.9Ų
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 933.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)