FAIRMol

KB_Leish_28

Pose ID 13654 Compound 3591 Pose 96

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
T21
T. cruzi R5P T. cruzi
Ligand KB_Leish_28
PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
41.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.75, H-bond role recall 0.56
Burial
66%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
2 protein-contact clashes 48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.764 kcal/mol/HA) ✓ Good fit quality (FQ -7.29) ✓ Good H-bonds (4 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Extreme strain energy (41.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-22.155
kcal/mol
LE
-0.764
kcal/mol/HA
Fit Quality
-7.29
FQ (Leeson)
HAC
29
heavy atoms
MW
406
Da
LogP
3.76
cLogP
Final rank
2.4574
rank score
Inter norm
-0.832
normalised
Contacts
14
H-bonds 8
Strain ΔE
41.2 kcal/mol
SASA buried
66%
Lipo contact
79% BSA apolar/total
SASA unbound
669 Ų
Apolar buried
350 Ų

Interaction summary

HBA 4 HY 2 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap12Native recall0.86
Jaccard0.75RMSD-
HB strict7Strict recall0.58
HB same residue+role5HB role recall0.56
HB same residue5HB residue recall0.62

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
96 2.457438655919487 -0.83199 -22.1549 8 14 12 0.86 0.56 - no Current
66 5.476807404947377 -0.826375 -22.5102 11 16 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 -22.155kcal/mol
Ligand efficiency (LE) -0.7640kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.293
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 406.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.76
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 41.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -6.45kcal/mol
Minimised FF energy -47.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 669.4Ų
Total solvent-accessible surface area of free ligand
BSA total 443.0Ų
Buried surface area upon binding
BSA apolar 349.8Ų
Hydrophobic contacts buried
BSA polar 93.2Ų
Polar contacts buried
Fraction buried 66.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2227.9Ų
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 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 766.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)