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 high
Native strong
SASA done
Strain ΔE
16.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.58, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
37% of hydrophobic surface appears solvent-exposed (7/19 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 (-1.190 kcal/mol/HA)
✓ Good fit quality (FQ -11.10)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (16.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-32.134
kcal/mol
LE
-1.190
kcal/mol/HA
Fit Quality
-11.10
FQ (Leeson)
HAC
27
heavy atoms
MW
396
Da
LogP
3.08
cLogP
Interaction summary
HB 11
HY 7
PI 1
CLASH 1
⚠ Exposure 36%
Interaction summary
HB 11
HY 7
PI 1
CLASH 1
⚠ Exposure 36%
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 12
Exposed 7
LogP 3.08
H-bonds 11
Exposed fragments:
aliphatic chain/group (7 atoms exposed)
| Final rank | 2.164 | Score | -32.134 |
|---|---|---|---|
| Inter norm | -1.157 | Intra norm | -0.033 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 11 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash | ||
| Residues |
ALA158
ALA24
ASN126
ASP129
GLN42
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
LEU130
LYS127
LYS159
LYS26
PHE38
SER27
SER28
THR44
THR69
| ||
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 | ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 515 | 1.0230320646141013 | -0.888421 | -24.9148 | 5 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 507 | 1.672453021099172 | -1.22174 | -32.1453 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 513 | 2.1636317836141687 | -1.15688 | -32.1344 | 11 | 20 | 15 | 0.71 | 0.45 | - | no | Current |
| 490 | 2.4947067608162152 | -1.08393 | -29.5116 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.134kcal/mol
Ligand efficiency (LE)
-1.1902kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.104
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
396.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-6.23kcal/mol
Minimised FF energy
-22.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
642.7Ų
Total solvent-accessible surface area of free ligand
BSA total
531.3Ų
Buried surface area upon binding
BSA apolar
363.0Ų
Hydrophobic contacts buried
BSA polar
168.2Ų
Polar contacts buried
Fraction buried
82.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1316.9Ų
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
511.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)