FAIRMol

KB_Leish_36

Pose ID 8961 Compound 1287 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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand KB_Leish_36
PDB1NJJ↗

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 high Native strong SASA done
Strain ΔE
24.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.42, H-bond role recall 0.20
Burial
84%
Hydrophobic fit
89%
Reason: no major geometry red flags detected
1 protein-contact clashes 42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.867 kcal/mol/HA) ✓ Good fit quality (FQ -7.99) ✓ Good H-bonds (4 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ High strain energy (24.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-22.550
kcal/mol
LE
-0.867
kcal/mol/HA
Fit Quality
-7.99
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.08
cLogP
Final rank
2.8980
rank score
Inter norm
-0.856
normalised
Contacts
19
H-bonds 4
Strain ΔE
24.1 kcal/mol
SASA buried
84%
Lipo contact
89% BSA apolar/total
SASA unbound
627 Ų
Apolar buried
469 Ų

Interaction summary

HBD 2 HBA 2 HY 3 PI 0 CLASH 1

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap10Native recall0.67
Jaccard0.42RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
33 1.6930652387964553 -1.3032 -33.8634 6 17 0 0.00 0.00 - no Open
25 2.37677582883771 -1.09051 -30.1724 6 17 0 0.00 0.00 - no Open
12 2.44585948723262 -0.900816 -20.7969 5 15 0 0.00 0.00 - no Open
35 2.5616248823522323 -0.851804 -21.5439 6 20 9 0.60 0.20 - no Open
153 2.897957358189819 -0.8562 -22.5503 4 19 10 0.67 0.20 - no Current
111 3.0202415484740994 -1.0648 -31.0336 6 17 0 0.00 0.00 - no Open
24 3.3091876015919386 -1.08568 -25.0988 6 16 0 0.00 0.00 - no Open
19 3.4171330511542393 -0.834551 -20.0158 4 11 0 0.00 0.00 - no Open
95 3.4786804256067114 -1.14676 -28.8385 7 19 0 0.00 0.00 - no Open
124 3.6213626191011485 -0.903161 -25.3504 6 14 0 0.00 0.00 - no Open
17 3.6275869878240954 -0.920544 -21.0159 12 15 0 0.00 0.00 - no Open
148 3.89202282370617 -0.806911 -21.6887 5 10 0 0.00 0.00 - no Open
25 4.022373065804421 -0.812568 -20.336 5 10 0 0.00 0.00 - no Open
27 4.286510035161286 -1.21476 -29.2815 7 19 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 -22.550kcal/mol
Ligand efficiency (LE) -0.8673kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.991
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.08
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -136.84kcal/mol
Minimised FF energy -160.92kcal/mol

SASA & burial

✓ computed
SASA (unbound) 627.1Ų
Total solvent-accessible surface area of free ligand
BSA total 526.5Ų
Buried surface area upon binding
BSA apolar 468.9Ų
Hydrophobic contacts buried
BSA polar 57.6Ų
Polar contacts buried
Fraction buried 84.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 89.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2533.2Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1373.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)