FAIRMol

KB_chagas_54

Pose ID 4912 Compound 3036 Pose 171

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_54
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
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
15.3 kcal/mol
Protein clashes
3
Internal clashes
6
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.40
Burial
87%
Hydrophobic fit
91%
Reason: 6 internal clashes
3 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.119 kcal/mol/HA) ✓ Good fit quality (FQ -10.56) ✓ Good H-bonds (4 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Moderate strain (15.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (14)
Score
-31.328
kcal/mol
LE
-1.119
kcal/mol/HA
Fit Quality
-10.56
FQ (Leeson)
HAC
28
heavy atoms
MW
510
Da
LogP
4.70
cLogP
Strain ΔE
15.3 kcal/mol
SASA buried
87%
Lipo contact
91% BSA apolar/total
SASA unbound
687 Ų
Apolar buried
545 Ų

Interaction summary

HB 4 HY 19 PI 1 CLASH 6

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 rank0.978Score-31.328
Inter norm-1.189Intra norm0.063
Top1000noExcludedno
Contacts13H-bonds4
Artifact reasongeometry warning; 14 clashes; 4 protein contact clashes; 4 cofactor-context clashes
Residues
ALA96 ARG14 ASP161 HIS35 LEU208 LEU209 LYS13 NAP301 PHE97 PRO210 SER37 SER95 TYR174

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 strict2Strict recall0.33
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
171 0.9784121004771374 -1.1891 -31.3276 4 13 9 0.47 0.40 - no Current
141 1.8729061917141898 -0.839296 -16.6469 3 15 0 0.00 0.00 - no Open
103 3.91503943863124 -1.21632 -28.798 6 22 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 -31.328kcal/mol
Ligand efficiency (LE) -1.1188kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.562
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 509.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.70
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 15.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 34.73kcal/mol
Minimised FF energy 19.44kcal/mol

SASA & burial

✓ computed
SASA (unbound) 687.2Ų
Total solvent-accessible surface area of free ligand
BSA total 596.0Ų
Buried surface area upon binding
BSA apolar 545.0Ų
Hydrophobic contacts buried
BSA polar 51.0Ų
Polar contacts buried
Fraction buried 86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 91.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1706.5Ų
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 972.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)