FAIRMol

KB_chagas_132

Pose ID 4208 Compound 108 Pose 145

DB SELECTIONDocking 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
T07
T. brucei PTR1 T. brucei
Ligand KB_chagas_132
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
22.2 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
78%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.811 kcal/mol/HA) ✓ Good fit quality (FQ -8.11) ✓ Good H-bonds (3 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (22.2 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (15)
Score
-27.564
kcal/mol
LE
-0.811
kcal/mol/HA
Fit Quality
-8.11
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
2.21
cLogP
Strain ΔE
22.2 kcal/mol
SASA buried
81%
Lipo contact
78% BSA apolar/total
SASA unbound
768 Ų
Apolar buried
486 Ų

Interaction summary

HB 3 HY 24 PI 3 CLASH 3
Final rank1.400Score-27.564
Inter norm-0.884Intra norm0.073
Top1000noExcludedno
Contacts16H-bonds3
Artifact reasongeometry warning; 15 clashes; 4 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 22.2
Residues
ALA212 ARG14 CYS168 GLU217 GLY214 LEU208 LEU209 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 TRP221 VAL206

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
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

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 strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
116 0.9967124239667426 -0.835107 -24.9422 1 19 0 0.00 0.00 - no Open
145 1.3995751921199313 -0.88415 -27.5642 3 16 13 0.68 0.00 - no Current
182 1.4861130235883124 -0.855269 -26.7745 4 22 0 0.00 0.00 - no Open
140 1.615020829250697 -0.925503 -28.3157 6 17 0 0.00 0.00 - no Open
161 2.662027008092362 -0.751934 -23.4535 3 14 0 0.00 0.00 - no Open
149 3.0092960382301914 -0.757482 -21.0618 2 22 0 0.00 0.00 - no Open
117 3.133913752613804 -0.893126 -27.6382 10 20 0 0.00 0.00 - no Open
92 3.1897154297188073 -0.7343 -24.0617 7 15 0 0.00 0.00 - no Open
109 3.266242765469782 -0.81009 -22.6151 5 16 0 0.00 0.00 - no Open
95 3.6098926606982675 -0.795677 -23.8078 8 16 0 0.00 0.00 - no Open
150 3.6690791561020983 -0.768661 -24.4817 6 18 0 0.00 0.00 - no Open
91 3.8086261390469938 -0.740979 -20.0503 5 21 0 0.00 0.00 - no Open
124 4.692634237226219 -0.64544 -22.9491 7 15 0 0.00 0.00 - no Open
103 4.725842136853786 -0.76159 -22.4824 5 18 0 0.00 0.00 - no Open
118 4.790784883872673 -0.731769 -21.8142 8 17 0 0.00 0.00 - no Open
73 4.7962875837914805 -1.009 -30.2636 11 20 0 0.00 0.00 - no Open
46 5.044122438992116 -0.80531 -23.3978 7 15 0 0.00 0.00 - no Open
87 5.0598912182116695 -0.712441 -22.3133 4 21 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 -27.564kcal/mol
Ligand efficiency (LE) -0.8107kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.112
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 47.95kcal/mol
Minimised FF energy 25.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 768.5Ų
Total solvent-accessible surface area of free ligand
BSA total 619.5Ų
Buried surface area upon binding
BSA apolar 486.4Ų
Hydrophobic contacts buried
BSA polar 133.1Ų
Polar contacts buried
Fraction buried 80.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1719.9Ų
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 942.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)