FAIRMol

Z1537384907

Pose ID 14776 Compound 2095 Pose 538

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
T22
L. donovani rab5a L. donovani
Ligand Z1537384907

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
10.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.36
Burial
89%
Hydrophobic fit
88%
Reason: no major geometry red flags detected
1 protein-contact clashes 77% of hydrophobic surface is solvent-exposed (17/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.216 kcal/mol/HA) ✓ Good fit quality (FQ -11.21) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Moderate strain (10.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-31.620
kcal/mol
LE
-1.216
kcal/mol/HA
Fit Quality
-11.21
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
4.36
cLogP
Strain ΔE
10.7 kcal/mol
SASA buried
89%
Lipo contact
88% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
502 Ų

Interaction summary

HB 6 HY 4 PI 1 CLASH 1 ⚠ Exposure 77%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
77% of hydrophobic surface is solvent-exposed (17/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 22 Buried (contacted) 5 Exposed 17 LogP 4.36 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
Final rank1.909Score-31.620
Inter norm-1.263Intra norm0.047
Top1000noExcludedno
Contacts19H-bonds6
Artifact reasongeometry warning; 13 clashes; 1 protein clash
Residues
ALA158 ALA24 ALA70 ASN126 ASP129 ASP68 GLU73 GLY23 GLY25 GLY71 LEU130 LYS127 LYS159 LYS26 PHE38 SER27 SER28 THR44 THR69

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap14Native recall0.67
Jaccard0.54RMSD-
HB strict5Strict recall0.33
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
524 0.5905835506967564 -0.910304 -24.2391 1 17 0 0.00 0.00 - no Open
513 1.7811485430227114 -1.13322 -25.8302 2 12 0 0.00 0.00 - no Open
538 1.9087060180372954 -1.2628 -31.6204 6 19 14 0.67 0.36 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -31.620kcal/mol
Ligand efficiency (LE) -1.2162kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.205
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.36
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 43.35kcal/mol
Minimised FF energy 32.61kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.2Ų
Total solvent-accessible surface area of free ligand
BSA total 568.9Ų
Buried surface area upon binding
BSA apolar 502.2Ų
Hydrophobic contacts buried
BSA polar 66.7Ų
Polar contacts buried
Fraction buried 88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1433.9Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 500.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)