FAIRMol

KB_chagas_115

Pose ID 8982 Compound 4115 Pose 174

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_chagas_115
PDB1NJJ↗

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 high Native strong SASA done
Strain ΔE
21.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.73, Jaccard 0.58, H-bond role recall 0.20
Burial
76%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
1 protein-contact clashes 52% of hydrophobic surface appears solvent-exposed (14/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.540 kcal/mol/HA) ✓ Good fit quality (FQ -5.36) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ High strain energy (21.9 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (15)
Score
-17.813
kcal/mol
LE
-0.540
kcal/mol/HA
Fit Quality
-5.36
FQ (Leeson)
HAC
33
heavy atoms
MW
446
Da
LogP
2.33
cLogP
Strain ΔE
21.9 kcal/mol
SASA buried
76%
Lipo contact
88% BSA apolar/total
SASA unbound
817 Ų
Apolar buried
551 Ų

Interaction summary

HB 7 HY 11 PI 0 CLASH 1 ⚠ Exposure 51%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
⚠️Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (14/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27 Buried (contacted) 13 Exposed 14 LogP 2.33 H-bonds 7
Exposed fragments: phenyl (5/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
Final rank1.881Score-17.813
Inter norm-0.668Intra norm0.128
Top1000noExcludedno
Contacts15H-bonds7
Artifact reasongeometry warning; 15 clashes; 5 protein contact clashes
Residues
ARG22 ARG242 ARG342 ASP243 ASP385 CYS26 GLN341 GLU343 GLU384 LEU25 LEU382 SER282 THR21 THR241 THR285

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 overlap11Native recall0.73
Jaccard0.58RMSD-
HB strict0Strict recall0.00
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
174 1.8806002512686402 -0.667633 -17.8132 7 15 11 0.73 0.20 - no Current
142 3.356493477450131 -0.796668 -22.2568 4 18 0 0.00 0.00 - no Open
182 3.964689923326005 -0.591868 -15.0424 6 11 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 -17.813kcal/mol
Ligand efficiency (LE) -0.5398kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.356
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 445.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.33
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 132.62kcal/mol
Minimised FF energy 110.67kcal/mol

SASA & burial

✓ computed
SASA (unbound) 816.5Ų
Total solvent-accessible surface area of free ligand
BSA total 624.3Ų
Buried surface area upon binding
BSA apolar 551.2Ų
Hydrophobic contacts buried
BSA polar 73.1Ų
Polar contacts buried
Fraction buried 76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2708.0Ų
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 1379.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)