FAIRMol

KB_Leish_75

Pose ID 4894 Compound 967 Pose 153

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_Leish_75
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
16.5 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.68, Jaccard 0.57, H-bond role recall 0.20
Burial
90%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.999 kcal/mol/HA) ✓ Good fit quality (FQ -9.91) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Moderate strain (16.5 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (15)
Score
-32.961
kcal/mol
LE
-0.999
kcal/mol/HA
Fit Quality
-9.91
FQ (Leeson)
HAC
33
heavy atoms
MW
456
Da
LogP
2.42
cLogP
Strain ΔE
16.5 kcal/mol
SASA buried
90%
Lipo contact
89% BSA apolar/total
SASA unbound
743 Ų
Apolar buried
595 Ų

Interaction summary

HB 2 HY 24 PI 1 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 rank1.215Score-32.961
Inter norm-1.055Intra norm0.056
Top1000noExcludedno
Contacts17H-bonds2
Artifact reasongeometry warning; 15 clashes; 4 protein contact clashes; 3 cofactor-context clashes
Residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LEU263 LYS13 MET163 MET213 NAP301 PHE97 PRO210 TRP221 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 overlap13Native recall0.68
Jaccard0.57RMSD-
HB strict1Strict recall0.17
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
153 1.2150235959287612 -1.05482 -32.9605 2 17 13 0.68 0.20 - no Current
151 2.8099851751413043 -0.767188 -23.2037 3 17 0 0.00 0.00 - no Open
121 3.0971385359136208 -0.761701 -19.6105 3 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 -32.961kcal/mol
Ligand efficiency (LE) -0.9988kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.910
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 455.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.42
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 63.06kcal/mol
Minimised FF energy 46.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 743.3Ų
Total solvent-accessible surface area of free ligand
BSA total 669.0Ų
Buried surface area upon binding
BSA apolar 595.0Ų
Hydrophobic contacts buried
BSA polar 74.0Ų
Polar contacts buried
Fraction buried 90.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1767.7Ų
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 952.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)