Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
19.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.95, Jaccard 0.77, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.286 kcal/mol/HA)
✓ Good fit quality (FQ -12.00)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (19.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (9)
✗ Internal clashes (8)
Score
-34.732
kcal/mol
LE
-1.286
kcal/mol/HA
Fit Quality
-12.00
FQ (Leeson)
HAC
27
heavy atoms
MW
361
Da
LogP
2.25
cLogP
Interaction summary
HB 8
HY 7
PI 1
CLASH 5
⚠ Exposure 47%
Interaction summary
HB 8
HY 7
PI 1
CLASH 5
⚠ Exposure 47%
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
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 10
Exposed 9
LogP 2.25
H-bonds 8
Exposed fragments:
pyridyl (5/6 atoms exposed)pyridyl (2/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.269 | Score | -34.732 |
|---|---|---|---|
| Inter norm | -1.207 | Intra norm | -0.080 |
| Top1000 | no | Excluded | no |
| Contacts | 25 | H-bonds | 8 |
| Artifact reason | geometry warning; 8 clashes; 9 protein contact clashes | ||
| Residues |
ALA158
ALA24
ALA40
ALA70
ASN126
ASN41
ASP129
ASP68
GLN42
GLU21
GLU73
GLY23
GLY25
GLY71
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
THR44
THR69
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 20 | Native recall | 0.95 |
| Jaccard | 0.77 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU: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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 243 | 0.6383642184233481 | -1.0895 | -32.0384 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 201 | 0.8514219575329248 | -1.05836 | -31.6861 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 226 | 0.9119370131705961 | -1.00589 | -29.0088 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 252 | 0.9771214741373022 | -0.806834 | -22.1243 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 230 | 1.2472816895024497 | -0.89324 | -26.0279 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 212 | 1.2689902355634186 | -1.20655 | -34.7324 | 8 | 25 | 20 | 0.95 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-34.732kcal/mol
Ligand efficiency (LE)
-1.2864kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.002
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
361.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.25
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.52kcal/mol
Minimised FF energy
55.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
647.5Ų
Total solvent-accessible surface area of free ligand
BSA total
599.9Ų
Buried surface area upon binding
BSA apolar
527.0Ų
Hydrophobic contacts buried
BSA polar
72.9Ų
Polar contacts buried
Fraction buried
92.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1421.5Ų
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
503.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)