FAIRMol

KB_Leish_127

Pose ID 1504 Compound 1281 Pose 149

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
T03
L. major DHFR L. major
Ligand KB_Leish_127

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.48, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.018 kcal/mol/HA) ✓ Good fit quality (FQ -9.25) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (17.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-25.437
kcal/mol
LE
-1.018
kcal/mol/HA
Fit Quality
-9.25
FQ (Leeson)
HAC
25
heavy atoms
MW
355
Da
LogP
4.11
cLogP
Strain ΔE
17.4 kcal/mol
SASA buried
76%
Lipo contact
81% BSA apolar/total
SASA unbound
632 Ų
Apolar buried
393 Ų

Interaction summary

HB 7 HY 18 PI 2 CLASH 1

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 rank2.334Score-25.437
Inter norm-1.064Intra norm0.046
Top1000noExcludedno
Contacts11H-bonds7
Artifact reasongeometry warning; 8 clashes; 2 protein clashes
Residues
ARG97 ASP52 ILE45 LEU94 LYS57 MET53 PHE56 PHE91 PRO50 PRO88 THR54

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap10Native recall0.50
Jaccard0.48RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
131 0.20264515361431967 -0.94386 -22.1 0 18 1 0.05 0.00 - no Open
149 2.3344907404766513 -1.06356 -25.4369 7 11 10 0.50 0.20 - no Current
124 2.946625187207625 -0.972192 -22.4238 7 15 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 -25.437kcal/mol
Ligand efficiency (LE) -1.0175kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.250
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 355.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.11
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 2.58kcal/mol
Minimised FF energy -14.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 632.5Ų
Total solvent-accessible surface area of free ligand
BSA total 482.9Ų
Buried surface area upon binding
BSA apolar 392.9Ų
Hydrophobic contacts buried
BSA polar 90.0Ų
Polar contacts buried
Fraction buried 76.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1528.7Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 833.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)