FAIRMol

KB_chagas_32

Pose ID 4908 Compound 1687 Pose 167

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 KB_chagas_32
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
23.9 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.58, Jaccard 0.52, H-bond role recall 0.40
Burial
89%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
3 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.136 kcal/mol/HA) ✓ Good fit quality (FQ -10.60) ✓ Good H-bonds (3 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ High strain energy (23.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (9)
Score
-30.672
kcal/mol
LE
-1.136
kcal/mol/HA
Fit Quality
-10.60
FQ (Leeson)
HAC
27
heavy atoms
MW
361
Da
LogP
3.10
cLogP
Strain ΔE
23.9 kcal/mol
SASA buried
89%
Lipo contact
89% BSA apolar/total
SASA unbound
628 Ų
Apolar buried
495 Ų

Interaction summary

HB 3 HY 21 PI 4 CLASH 5

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 rank0.378Score-30.672
Inter norm-1.287Intra norm0.151
Top1000noExcludedno
Contacts13H-bonds3
Artifact reasongeometry warning; 9 clashes; 4 protein contact clashes; 4 cofactor-context clashes; moderate strain Δ 23.9
Residues
ARG14 ASP161 LEU208 LEU209 LYS13 NAP301 PHE97 PRO210 SER207 SER95 TYR174 VAL206 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 overlap11Native recall0.58
Jaccard0.52RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
167 0.3777883732091702 -1.28702 -30.6719 3 13 11 0.58 0.40 - no Current
132 0.4874910028978664 -1.12202 -29.4868 3 16 14 0.74 0.20 - no Open
75 0.5397889905628415 -0.918241 -19.8042 4 14 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 -30.672kcal/mol
Ligand efficiency (LE) -1.1360kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.598
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 361.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.10
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 125.63kcal/mol
Minimised FF energy 101.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 628.4Ų
Total solvent-accessible surface area of free ligand
BSA total 557.0Ų
Buried surface area upon binding
BSA apolar 495.1Ų
Hydrophobic contacts buried
BSA polar 61.9Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1680.0Ų
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 936.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)